I have the exact same problem with my installation. Same version of ISPConfig with me too. My install should be as clean as it can be (installed only two days ago to a blank Ubuntu 12.04 server). When I remove the site and check the /etc/fstab file, the mountpoint to the logfile has been removed, but if I type "mount" I still see the mount connection existing and this prevents the directory removal.
So it seems that the apache2_plugin.inc.php script is not able to execute the exec('umount...') command for the mountpoint removal. But the script is able to remove the line from the fstab though..
Anyone else having the same problem? Any resolution for this? Could it be that the userid the php-script is being executed (is it the www-data or the ispconfig user?) does not have proper access to umount -command?