Can you take a look at this Weilun? Seems like it's only present on local NTP.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/8206d7a22f5510c8a491a19f737f9ba4b4e2cc9d

commit 8206d7a22f5510c8a491a19f737f9ba4b4e2cc9d
Author: Weilun Shi <sweilun@chromium.org>
Date: Sat Sep 29 01:16:14 2018

[NTP] Prevent notification bar disappear with existing notification bar

After trigger the existing one's timeout, the existing one's will add
the "hide" class to the bar that makes both of them disappear because
they share the same notification bar. Instead of triggering the old one,
we clear the timeout and replace it with the new one.

Screencast:
https://screencast.googleplex.com/cast/NjQzMTIwODQ1NjA2MDkyOHw4ODNkMjg4OS01OA

Bug:  889257 
Change-Id: Ifb6b5a0acb2f68470cc80ef1bea0c6e176f34bcb
Reviewed-on: https://chromium-review.googlesource.com/1252462
Commit-Queue: Weilun Shi <sweilun@chromium.org>
Reviewed-by: Kristi Park <kristipark@chromium.org>
Cr-Commit-Position: refs/heads/master@{#595280}
[modify] https://crrev.com/8206d7a22f5510c8a491a19f737f9ba4b4e2cc9d/chrome/browser/resources/local_ntp/local_ntp.js

@sweilun@chromium.org : Could you please provide manual reproducible steps to verify the fix from our end. It would be really helpful if provided a sample URL/ Test file to verify the fix.

Thanks..!

1) Add a new custom link through "Add short tile" or modify an existing custom link through the three dot menu. See a notification bar floats up from the bottom.
2) Repeat the (1) multiple times. The notification bar should not disappear and the previous notification bar will be replaced by the new one, especially the timeout. The last one should disappear in 10 sec if no further actions.

Tried verifying the fix on the build without fix #71.0.3561.0 on Window 10 by followed steps as per comment #6, but unable to observe the difference between both builds. As we are Observed that The notification bar disappears.
Attached the screenshots for reference.
sweilun@chromium.org@ - Could you please help in verifying the fix.

Thanks..!

Deleted: 889257.mp4 3.3 MB

	889257.mp4 3.3 MB View Download

This CL has not landed on Official Build yet. Please verify it on the latest canary or chromium. Thanks!