Turns out this is an issue with synchronizing the active and pending trees on the impl thread, rather than with viewport anchoring on the main thread. I've got a fix ready but there's some other subtle issues I've discovered so I'll try to fix them all in one go.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/fe9e63ecc3b6d320006ba0d22b7000eb0af30239

commit fe9e63ecc3b6d320006ba0d22b7000eb0af30239
Author: bokan <bokan@chromium.org>
Date: Tue Jul 19 19:19:08 2016

Update scroll layers' bounds_delta earlier during tree activation.

When a tree activation occurs, we must update the property trees' bounds deltas
so that they get propagated across the trees. This was previously done in
LayerTreeHostImpl::ActivateSyncTree() and needs to happen before
updateViewportContainerSizes() is called, otherwise it will clamp scroll offsets
incorrectly becaues the bounds_deltas haven't been propagated yet.

However, this bug occurs because earlier in ActivateSyncTree(), in
LayerTreeImpl::PushPropertiesTo, we may change the top controls values when
PushTopControls is called and causes a change. This indirectly causes
UpdateViewportContainerSizes to be called which we must do after updating the
bounds deltas.

This CL moves the update to happen inside LayerTreeImpl::PushPropertiesTo near
the beginning. I've rewritten the ViewportBoundsDeltaOnTreeActivation test to
catch this. It was written to catch basically the same issue but with
UpdateViewportContainerSizes being called later than in this bug so checking for
this case should catch both.

BUG= 627911 
CQ_INCLUDE_TRYBOTS=tryserver.blink:linux_blink_rel

Review-Url: https://codereview.chromium.org/2149033002
Cr-Commit-Position: refs/heads/master@{#406341}

[modify] https://crrev.com/fe9e63ecc3b6d320006ba0d22b7000eb0af30239/cc/trees/layer_tree_host_impl.cc
[modify] https://crrev.com/fe9e63ecc3b6d320006ba0d22b7000eb0af30239/cc/trees/layer_tree_host_impl_unittest.cc
[modify] https://crrev.com/fe9e63ecc3b6d320006ba0d22b7000eb0af30239/cc/trees/layer_tree_impl.cc