The ispconfig interface should not be run with suphp. My guess is that suphp is enabled globally by accident on your server. Edit the suphp.conf file in /etc/apache2/mods-available and remove any addtype and addhandler lines that you find there. Then restart apache and undo the changes you described above.
Remains in my logs hundreds of lines of this type, but it must be another problem...
Which ispconfig version do you use?