AppArmor is one of those things that our distribution engineers like to put into our Linux distributions without telling us. If you don't know about it, it can cause some WEIRD errors.
First off, AppArmor is basically another more restrictive set of file permissions, based not on the userid, but the filename of the process itself. If a process is not allowed access to a file by AppArmor, it will fail, just as if the permissions were set wrong.
If you don't know about this, it can be a head scratcher. Like for instance, I just moved my MySQL tables from their natural home to the raid. All the permissions are set properly, because mv does that when it can, and because I was root at the time. But MySQL still wouldn't work.
There is a set of file restrictions in /etc/apparmor.d/ . Find the right file, named after the process path but with dots instead of slashes (/etc/apparmor.d/.usr.bin.mysqld controls access by /usr/bin/mysqld). Set the permissions in there, and things will work.
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