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.
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Remains in my logs hundreds of lines of this type, but it must be another problem...
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Which ispconfig version do you use?