Evan, could this be related to your recent changes to the bookmarks bar?

https://chromiumcodereview.appspot.com/1820793003/
and
https://chromiumcodereview.appspot.com/1823623003/

If nothing jumps out as the cause I can perform a bisect.

Related?

https://bugs.chromium.org/p/chromium/issues/detail?id=596122

This is actually happening on Chrome OS 50.0.2661.50 beta branch, my guess is that it would be from a recent merge by estade@. Evan do you know the root cause of this? If not please let me know and I will do some digging.

Yes I bet it's related to the change that made the bookmark bar paint to a layer, but I'm not sure what to do about it. We need to somehow tell ripple layers to have a higher z order (not just relative to their sibling layers, but also to cousin layers).

tehmaxhypegaming@, sorry I missed your comment (#2).  Issue 596122  is unrelated to this one.

Review: https://codereview.chromium.org/1849563002/

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/52ef1ab0da46ea871271a0a2a6fa0ced541b0381

commit 52ef1ab0da46ea871271a0a2a6fa0ced541b0381
Author: bruthig <bruthig@chromium.org>
Date: Sat Apr 02 13:57:38 2016

The Material Design ink drops on the ToolbarView are supposed to expand beyond the bounds of the ToolbarView and should be visible above the BookmarkBarView.

BUG= 597757 
TEST=Manual

Review URL: https://codereview.chromium.org/1849563002

Cr-Commit-Position: refs/heads/master@{#384808}

[modify] https://crrev.com/52ef1ab0da46ea871271a0a2a6fa0ced541b0381/chrome/browser/ui/views/frame/browser_view.cc

Your change meets the bar and is auto-approved for M50 (branch: 2661)

Please merge your change to M50 branch 2661 by 5:00 PM on Monday, 04/04/16 so we can take it for next week beta. Thank you.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/c3a6d1ef7c91fd4fce9e3a171739e8134996e524

commit c3a6d1ef7c91fd4fce9e3a171739e8134996e524
Author: Ben Ruthig <bruthig@chromium.org>
Date: Mon Apr 04 15:16:19 2016

The Material Design ink drops on the ToolbarView are supposed to expand beyond the bounds of the ToolbarView and should be visible above the BookmarkBarView.

BUG= 597757 
TEST=Manual

Review URL: https://codereview.chromium.org/1849563002

Cr-Commit-Position: refs/heads/master@{#384808}
(cherry picked from commit 52ef1ab0da46ea871271a0a2a6fa0ced541b0381)

Review URL: https://codereview.chromium.org/1853173002 .

Cr-Commit-Position: refs/branch-heads/2661@{#472}
Cr-Branched-From: ef6f6ae5e4c96622286b563658d5cd62a6cf1197-refs/heads/master@{#378081}

[modify] https://crrev.com/c3a6d1ef7c91fd4fce9e3a171739e8134996e524/chrome/browser/ui/views/frame/browser_view.cc

Tested the same on win8.1 and Linux 14.04 chrome version 51.0.2700.0 by enabling #top-chrome-md flag to "material" in chrome://flags - observed no clipping of navigation buttons with the bookmark bar.

Please find the screenshot

Deleted: 597757.png 13.4 KB

	597757.png 13.4 KB View Download

Verified the issue on Win 7 and Ubuntu 14.04 and its working fine.
Attached the screen shot for the reference.Hence added the TE-Verified labels.

Deleted: 597757_April_6.png 51.2 KB

	597757_April_6.png 51.2 KB View Download

Verified the issue on Win 7 and Ubuntu 14.04 using 51.0.2704.22 and its working fine.Attached a screen cast for the same.

Deleted: 597757_April_21.mp4 867 KB

597757_April_21.mp4 867 KB Download

Verified on 50.0.2661.103/7878.74.0 Chrome OS