I do remember at one point several months ago I was using sshfs from a laptop to connect to the server's file system.... and it somehow messed up the permissions of my / directory (i think).
When this happened all of my websites went offline and I spend around an hour to figure out the problem. fixed the permission problem. and my websites were working again... I think this might have something to do with my problem now that I think back.
However I've given the phpmyadmin/ispconfig web application temporary 777 permissions and seems to be the same...