Same thing is happening to me. Just started after some package upgrades.
I have never touched the AppArmor config nor the MySQL config. I wound
up disabling AppArmor in the meantime just so that I can get my database
server up again.
Mar 03 20:09:28 oddnetwork.org audit[4215]: AVC apparmor="DENIED
My Gnome terminal also has a solid background on launch, and only by
either tweaking settings or using the Help -> About workaround will
bring the transparency back. Has been driving me crazy for a few
releases now. :(
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