This might get fixed as part of some other virtual keyboard bug?

Yes, I think so.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/0c5b078db1822183ca1a7bd35dd6c06a40a297db

commit 0c5b078db1822183ca1a7bd35dd6c06a40a297db
Author: Yuichiro Hanada <yhanada@chromium.org>
Date: Mon Dec 04 08:05:32 2017

Don't recreate VirtualKeyboardContainer window when activating VK.

Always create VirtualKeyboardContainer instead of creating on the fly,
so we can register it as an ActivationParent correctly.
This change also deletes code that checks the existence of virtual
keyboard by the existence of the container window.

The location of the container has been changed from between
ImeWindowParentContainer & KeyboardContainer, to between
VirtualKeyboardParentContainer and KeyboardContainer.
The new hierarchy is:
RootWindow ->
ScreenRotationContainer ->
LockScreenRelatedContainersContainer ->
VirtualKeyboardParentContainer ->
VirtualKeyboardContainer ->
KeyboardContainer (which is owned by KeyboardController) ->
keyboard contents window.

Bug:  731537 ,  616909 
Test: Unit tests pass.
Change-Id: Ia9d04fe3ef9b2584dfbe1b785b498f8152fc398b
Reviewed-on: https://chromium-review.googlesource.com/771470
Commit-Queue: Yuichiro Hanada <yhanada@chromium.org>
Reviewed-by: Mitsuru Oshima <oshima@chromium.org>
Cr-Commit-Position: refs/heads/master@{#521288}
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/BUILD.gn
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/public/cpp/shell_window_ids.h
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/root_window_controller.cc
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/root_window_controller.h
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/root_window_controller_unittest.cc
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/shell_unittest.cc
[add] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/virtual_keyboard_container_layout_manager.cc
[add] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/virtual_keyboard_container_layout_manager.h
[modify] https://crrev.com/0c5b078db1822183ca1a7bd35dd6c06a40a297db/ash/wm/always_on_top_controller_unittest.cc