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As some of you might now I've been having some trouble with my server that I was not able to track down, but 11 days ago I noticed that mysql was filling up my kernel logs, apparmor was preventing it from starting, flooding my logs with error messages.
I disabled Mysql completely - since it's not used on the server, and now it seems that was what was causing the trouble I've been having. It's been 11 days now, and no issues what so ever, so this looks promising.