I wasn't able to repro, but maybe Avi has some ideas? Could be a tab-modal dialog misbehaving.

Not able to reproduce here on Ubuntu.

After reading through all the latest comments, I tried to reproduce it again on my side and succeed. I have prepared video for the same, but cannot load that here as its size is ~64 MB. So please let me know how else I can share that video with you.

Can you put it on Google Drive or another storage service (YouTube, DropBox, etc.)?

Uploaded in Google Drive. Please get it from - https://drive.google.com/file/d/0B1nn8gJq67KhYU1CcXlpODJVLUk/view?usp=sharing

Ah, you need to have the devtools window docked.

I am not sure what you mean by docked, if it is as same as keeping open, then I am not sure whether certificate can be kept open without keeping devtools window open. 

But main step to re-pro this issue is keeping certificate open.

What I mean is that the devtools can be put into its own window, but if you do so then you can't reproduce this issue.

I can confirm this with the docked devtools window. This only appears to affect the area that would be covered by the sheet, not any other parts of the page.

This is probably because -hideSheet only sets the alpha value but doesn't do anything about event handling.

This is using a system sheet, not our constrained window... Can we switch it over?

If we look at certificate_viewer_mac.mm's -hideSheet and -unhideSheet, you'll see that they save and restore the sheet view's autoresizesSubviews value. Why? Because the certificate sheet used to not only be alpha-ed out but it used to be resized out, and resizing the sheet while autoresizesSubviews was set would break the layout. (See the similar code using oldResizesSubviews_ in ssl_client_certificate_selector_cocoa.mm's -hideSheet to see how it used to be done.) The oldResizesSubviews_ is unneeded if no resizing happens, but it was left as a remnant.

Resizing of the sheet was done explicitly to avoid this problem. Since spqchan removed the resizing code in https://codereview.chromium.org/1495623008, I'm assigning this bug to her.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/8fba1d4d58b4e12b1b99df85caf36332bdb4dc07

commit 8fba1d4d58b4e12b1b99df85caf36332bdb4dc07
Author: spqchan <spqchan@chromium.org>
Date: Fri Jun 03 18:13:35 2016

Fix Hiding Issue with Certificate Viewer Mac

Add removed code from https://codereview.chromium.org/1495623008
that changes the position of the viewer when it hides/unhides.

Added logic that calculates the x and y position offset of the dialog
when it unhides.

BUG= 611603 

Review-Url: https://codereview.chromium.org/2034993002
Cr-Commit-Position: refs/heads/master@{#397756}

[modify] https://crrev.com/8fba1d4d58b4e12b1b99df85caf36332bdb4dc07/chrome/browser/ui/cocoa/browser_window_controller_private.mm
[modify] https://crrev.com/8fba1d4d58b4e12b1b99df85caf36332bdb4dc07/chrome/browser/ui/cocoa/certificate_viewer_mac.h
[modify] https://crrev.com/8fba1d4d58b4e12b1b99df85caf36332bdb4dc07/chrome/browser/ui/cocoa/certificate_viewer_mac.mm
[modify] https://crrev.com/8fba1d4d58b4e12b1b99df85caf36332bdb4dc07/chrome/browser/ui/cocoa/certificate_viewer_mac_browsertest.mm

 Issue 609063  has been merged into this issue.

As this issue is fixed now, so I wonder whether this is been considered under any of your bounty programs or it doesn't meet the criteria.

Unfortunately, this does not meed the criteria for the security rewards program. It was a real bug, but it was not a security vulnerability. We currently only reward security vulnerabilities.

 Issue 641792  has been merged into this issue.