Sorry to hear about this problem, this does appear to be a bug. We have a ticket about this issue that you can see in CLOUD-10963. Please vote on that issue if you're affected by this problem.
Should a workaround become available or a fix be applied to Atlassian Cloud sites about this, I would expect that ticket to be updated to reflect this.
I was able to work around this, and eliminate the annoying message. The problem started when I logged in as an impersonation account. Instead of switching back, I logged out of the impersonation account and then logged back in with my native account. After doing that I received the annoying pop up every time I accessed the application.
So I used the following corrective process: I logged in again as the same impersonation account and then 'switched back'. This seems to be key because this corrected the problem. I no longer receive the annoying message when I log into the application.
Atlassian: You need to fix the logout function for an impersonation account to clear out whatever application state is cleared out by the 'switch back' function.
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