Using the per-revision bisect providing the bisect results,
Good build: 55.0.2844.0 (Revision: 415023).
Bad build: 55.0.2845.0 (Revision: 415522).

You are probably looking for a change made after 415131 (known good), but no later than 415132 (first known bad).
CHANGELOG URL:
  https://chromium.googlesource.com/chromium/src/+log/5da57202cf43d20b68566c6851043f2d83c99f58..b80d9eb6c3b98e374b2f8eef570094d66b3406ba

From the above CL, assigning the issue to concern owner,

Suspecting Commit# 35512aa7e4acc3ceb9c6aef5d61eebfb4ae802af
Suspecting Review URL# https://codereview.chromium.org/2273893002

@jaepark -- Could you please look into the issue, pardon me if it has nothing to do with your changes and if possible please assign it to concern owner.
Thank You.

+ mcnee@ ... could this be related to your change Kevin?

@wjmaclean, I just tested without my change and this bug still occurs. I'm guessing that this doesn't use SetLayerTransform, so it shouldn't hit my change at all.

Thanks for testing ... good to rule that out.

Thanks for checking. Yes, I'm the right owner.

The following revision refers to this bug:
  https://pdfium.googlesource.com/pdfium.git/+/c75dcd253d75ea93608410d90a3ce1b605590af0

commit c75dcd253d75ea93608410d90a3ce1b605590af0
Author: thestig <thestig@chromium.org>
Date: Mon Nov 14 21:15:47 2016

Invalidate a slightly larger rect when updating popup annotations.

It looks like sometimes there are rounding errors in the display
pipeline when displaying / hiding popup annotations. Compensate by
rouding up the damaged rect slightly.

BUG= chromium:662804 

Review-Url: https://codereview.chromium.org/2492733002

[modify] https://crrev.com/c75dcd253d75ea93608410d90a3ce1b605590af0/fpdfsdk/cpdfsdk_baannothandler.cpp

Should be fixed on trunk today. Will wait for QA to verify before requesting a merge.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/536cf7b135468bc3848faadae2b35089d22d46aa

commit 536cf7b135468bc3848faadae2b35089d22d46aa
Author: pdfium-deps-roller <pdfium-deps-roller@chromium.org>
Date: Tue Nov 15 03:49:39 2016

Roll src/third_party/pdfium/ e3c731526..343980241 (6 commits).

https://pdfium.googlesource.com/pdfium.git/+log/e3c731526c04..3439802410dc

$ git log e3c731526..343980241 --date=short --no-merges --format='%ad %ae %s'
2016-11-14 dsinclair Cleanup fwl_* classes and cfx_* classes in fwl.
2016-11-14 tsepez Make CPDF_PageContentGenerator methods take object numbers
2016-11-14 thestig Fix nits in CPDF_PageOrganizer.
2016-11-14 npm Fix some nits in pdfium_test
2016-11-14 thestig Invalidate a slightly larger rect when updating popup annotations.
2016-11-14 npm Properly release caches in CPDF_DocRenderData

BUG= 660756 , 662804 

Documentation for the AutoRoller is here:
https://skia.googlesource.com/buildbot/+/master/autoroll/README.md

If the roll is causing failures, see:
http://www.chromium.org/developers/tree-sheriffs/sheriff-details-chromium#TOC-Failures-due-to-DEPS-rolls

TBR=dsinclair@chromium.org

Review-Url: https://codereview.chromium.org/2499223002
Cr-Commit-Position: refs/heads/master@{#432083}

[modify] https://crrev.com/536cf7b135468bc3848faadae2b35089d22d46aa/DEPS

Still able to reproduce the issue on Windows-10, Mac 10.11.6 and Ubuntu 14.04 using latest dev #56.0.2922.0.

thestig@ - Could you please confirm on the fix.

Thanks...!!

The attached video is what I see here. It looks fixed to me.

Deleted: 1.avi 517 KB

1.avi 517 KB Download

krajshree@ - If it's not fixed, can you post a video to show what the bug looks like on your computer?

Verified this issue on Ubuntu 14.04 using chrome latest Dev M56-56.0.2924.0 by following steps mentioned in the original comment. Observed the outline of overlay is not seen while zooming the pdf page. Hence adding TE-Verified. 

thestig@ Issue is still seen on chrome latest M55-55.0.2883.59. Could you please merge the same fix to M-55 branch version.

Thanks!

Request to merge https://pdfium.googlesource.com/pdfium.git/+/c75dcd253d75ea93608410d90a3ce1b605590af0 for M55.

[Automated comment] DEPS changes referenced in bugdroid comments, needs manual review.

Approving merge to M55 branch 2883 based on comment #13. Please merge ASAP. Thank you.

Merged: https://pdfium.googlesource.com/pdfium/+/dad0707d0e7ea3f612dd14a5e35b5af163cedf82