Very similar to described issue with dns zone file location settings on 2.2.21
Just wanted to post a note about this.
I ran into nearly the same issue described above on version 2.2.21. I have installed and maintain many servers running ispconfig and this particular version seemed much more problematic than others, sometimes changes would not apply without restarting ispconfig and other oddities.
At one point I attempted upgrading to 2.2.24 but the upgrade hung and had to killed, and I had to restore the server to prior state via virtualization tools.
Then just recently no dns changes could be applied and the dns recycle bin and isp recycle bins could not be emptied, configuration files being updated endlessly, etc.
Noticed php segfaults in the logs, found the patch to downgrade to php5.0.4 for ispconfig operation, that worked but dns changes still could not be made. Also the path to dns zone files was incorrect but attempts to fix it were unsuccessful via the gui and had to be done directly in the database.
Finally reset permissions on zone files as follows: after finding a recommendation to do so:
chmod 755 /var/named/
chmod 775 /var/named/chroot/
chmod 775 /var/named/chroot/var/
chmod 755 /var/named/chroot/var/named/
chmod 775 /var/named/chroot/var/run/
chmod 777 /var/named/chroot/var/run/named/
then ran config file updates manually with:
/root/ispconfig/php/php -q /root/ispconfig/scripts/writeconf.php
and at that point all seems to be well
Upgrading to 2.2.26 was thereafter successful.
Hopefully this info is of use in case the issue arises in the future.