Unable to reproduce the issue in Mac 10.12.2, Win-10 and Ubuntu 14.04 by using chrome reported version #56.0.2924.28 and latest canary #57.0.2979.0.

Steps followed to reproduce the issue are as follows:
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1. Installed some extensions for e.g. honey and momentum
2. Deactivated them by unchecking the enabled checkbox.
3. Observed that after deactivating, both the extensions got removed from the toolbar. They were no more visible in the toolbar as expected.

Attaching screen cast for reference

dbonde@ - Could you please check this issue on latest canary #57.0.2979.0 by creating a new profile and please let us know if the issue still persist or not.

Thanks...!!

Deleted: 679374.mp4 850 KB

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"Could you please check this issue on latest canary #57.0.2979.0 by creating a new profile and please let us know if the issue still persist or not."

What if the profile is the problem (which is my guess)?

Thank you for providing more feedback. Adding requester "krajshree@chromium.org" for another review and adding "Needs-Review" label for tracking.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

Unable to reproduce the issue in Mac 10.12.2 chrome version 56.0.2924.67 and canary 58.0.2990.0		

It may be possible that the profile gets corrupted with some extensions/apps. You need to disable the extensions one by one to see which caused the problem and remove it.

Please update the thread with your observation.

I just made an observation.

After changing system language at restarting Chrome, only one extension was visible in the toolbar. This extension has a special story: initially it was downloaded from the Chrome Store but after an update an important feature disappeared so I wanted to revert to an old version (this is several years ago).

I extracted the old version of the extension from a backup and then "sideloaded" it into Chrome to "disconnect" it from Chrome Store to prevent future updates.

Every time I restart Chrome I am asked if I want to trust this old extension that is running in developer mode.

Anyway, this extension was the only one visible after the language change but after disabling it all expected extensions immediately reappeared in the toolbar, and remained there even after re-enabling this odd extension (that in itself is not, and should not, be visible in the toolbar). And now all deactivated extensions that used to show up after a restart are not visible, as expected.

I'm thinking that extensions that are active before a change of system language and then, after the switch of language, are deactivated are the ones that were visible when they shouldn't be.

Thank you for providing more feedback. Adding requester "tkonchada@chromium.org" to the cc list and removing "Needs-Feedback" label.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

As per comment #7, closing this issue as wont fix.

Please feel free to raise a new issue, if able to reproduce again.

Thanks...!!