This is due to the install path being autodetected incorrectly (it gets the whole /home/.server/yourusername thing wrong). The global variable $INSTALL_PATH needs to be manually set to your install path.
Go to index.php and change line 47 (i think) from:
$INSTALL_PATH = Dirname($SERVER['SCRIPTFILENAME']);
$INSTALL_PATH = '/home/username/your.domain.com';
Hope this helps. Also, I was previously using that ini thing that I found here in the forums, but I removed that after I changed my install path and things seem to be working fine.