Found out what the problem is, in ubuntu session.gc_probability is disabled or set to 0 by default. More people are probably going to be affected by this. I found this in the /etc/php5/apache2/php.ini file:
; This is disabled in the Debian packages, due to the strict permissions
; on /var/lib/php5. Instead of setting this here, see the cronjob at
; /etc/cron.d/php5, which uses the session.gc_maxlifetime setting below.
; php scripts using their own session.save_path should make sure garbage
; collection is enabled by setting session.gc_probability
;session.gc_probability = 0
I have set this to 1 now, I hope this fixes it, since ISPconfig sets the session storage path for each virtual host anyway.
Hope this helps other people as well!