Yesterday was a bad day for me. I did a really stupid thing.
Never ever mount your (web)server with root permissions under nautilus (with SSH) in your local home directory and chmod at the same time recursively your home.
Guess what happens?! It will automatically chmod all your files on your (web)server too! Remember being root there.
So, to make a long story short: I had to reinstall the whole thing after the nice people from vlinux.de did a fresh install of the virtual server. Luckily i could backup all the important data like the mysql-database or the emails. Maybe this is a good chance to try a different web-server, like cherokee? Lets see, if i can get everything back running as it was before.