Happy to help.
I thought it unlikely that calibre could have changed anything owned by the root user
so it isn't surprising that a new user worked, it is a commonly-used tactic to fix mysterious gremlins.
I do wonder what would be causing the icons to remain white on a clean user.
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If you want to investigate the causes, and/or simply restore the settings you had before, you can try logging in to the original user via the virtual console, moving selected dotfiles to backup locations (`mv ~/.config ~/.config.bak`), starting mate-session manually and seeing if it fixes the problem.
If not, quit Mate, delete the newly-generated ~/.config and move the backup back in place and try some other dotfiles.
If it did fix the problem, you can try narrowing down where in those dotfiles it happened, using the same process of elimination.
At the very least, you should be able to restore part or all of your custom configuration.
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If you do investigate, and discover anything useful like which particular corrupted files caused the strobing, we'd love to hear about it. And wherever the fault lies, I'm sure someone wants to fix their software so this doesn't happen again.