Not sure if this is related to the Media Drm stuff or not, but am hitting this on a few devices. Both my N5 on Marshmallow running a clean ToT build as well as on my old JellyBean tablet while navigating around media sites. Most recently I was trying to play this:

http://storage.googleapis.com/dalecurtis-shared/mse_clank/mse_mp4.html

[FATAL:embedded_application_runner.cc(66)] Check failed: application_thread_checker_.CalledOnValidThread(). 

Stack Trace:
  RELADDR   FUNCTION                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       FILE:LINE
  0008198b  ~LogMessage                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    /d/code/chrome/src/base/logging.cc:524
  0047a913  content::EmbeddedApplicationRunner::Instance::BindShellClientRequestOnApplicationThread(mojo::InterfaceRequest<shell::mojom::ShellClient>)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     /d/code/chrome/src/content/common/mojo/embedded_application_runner.cc:66
  003b9c07  void base::internal::RunnableAdapter<void (content::GpuChildThread::*)(mojo::InterfaceRequest<content::mojom::ProcessControl>)>::Run<content::GpuChildThread*, mojo::InterfaceRequest<content::mojom::ProcessControl> >(content::GpuChildThread*&&, mojo::InterfaceRequest<content::mojom::ProcessControl>&&)                                                                                                                                                                                                                                                                                                                                                                                                  /d/code/chrome/src/base/bind_internal.h:186
  v------>  void base::internal::InvokeHelper<false, void, base::internal::RunnableAdapter<void (content::EmbeddedApplicationRunner::Instance::*)(mojo::InterfaceRequest<shell::mojom::ShellClient>)> >::MakeItSo<scoped_refptr<content::EmbeddedApplicationRunner::Instance> const&, mojo::InterfaceRequest<shell::mojom::ShellClient> >(base::internal::RunnableAdapter<void (content::EmbeddedApplicationRunner::Instance::*)(mojo::InterfaceRequest<shell::mojom::ShellClient>)>, scoped_refptr<content::EmbeddedApplicationRunner::Instance> const&, mojo::InterfaceRequest<shell::mojom::ShellClient>&&)                                                                                                             /d/code/chrome/src/base/bind_internal.h:311
  0047aac5  base::internal::Invoker<base::IndexSequence<0u, 1u>, base::internal::BindState<base::internal::RunnableAdapter<void (content::EmbeddedApplicationRunner::Instance::*)(mojo::InterfaceRequest<shell::mojom::ShellClient>)>, void (content::EmbeddedApplicationRunner::Instance*, mojo::InterfaceRequest<shell::mojom::ShellClient>), content::EmbeddedApplicationRunner::Instance*, base::internal::PassedWrapper<mojo::InterfaceRequest<shell::mojom::ShellClient> > >, base::internal::InvokeHelper<false, void, base::internal::RunnableAdapter<void (content::EmbeddedApplicationRunner::Instance::*)(mojo::InterfaceRequest<shell::mojom::ShellClient>)> >, void ()>::Run(base::internal::BindStateBase*)  /d/code/chrome/src/base/bind_internal.h:362
  v------>  base::Callback<void (), (base::internal::CopyMode)1>::Run() const                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              /d/code/chrome/src/base/callback.h:397
  0006f12b  base::debug::TaskAnnotator::RunTask(char const*, base::PendingTask const&)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     /d/code/chrome/src/base/debug/task_annotator.cc:51
  00087aaf  base::MessageLoop::RunTask(base::PendingTask const&)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           /d/code/chrome/src/base/message_loop/message_loop.cc:478
  00087ccb  base::MessageLoop::DeferOrRunPendingTask(base::PendingTask const&)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             /d/code/chrome/src/base/message_loop/message_loop.cc:487
  00087f31  base::MessageLoop::DoWork()                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    /d/code/chrome/src/base/message_loop/message_loop.cc:604
  00089771  base::MessagePumpDefault::Run(base::MessagePump::Delegate*)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    /d/code/chrome/src/base/message_loop/message_pump_default.cc:33
  000877e1  base::MessageLoop::RunHandler()                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                /d/code/chrome/src/base/message_loop/message_loop.cc:442
  000a1e49  base::RunLoop::Run()                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           /d/code/chrome/src/base/run_loop.cc:35
  00086fef  base::MessageLoop::Run()                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       /d/code/chrome/src/base/message_loop/message_loop.cc:294
  000c29e7  base::Thread::ThreadMain()                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     /d/code/chrome/src/base/threading/thread.cc:254
  000be727  base::(anonymous namespace)::ThreadFunc(void*)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 /d/code/chrome/src/base/threading/platform_thread_posix.cc:70
  0000ca5b  <unknown>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      /system/lib/libc.so
  0000cbd7  <unknown>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      /system/lib/libc.so