i have a similar problem with this thread http://www.howtoforge.com/forums/showthread.php?t=44694
(which is not solved)
rkhunter and fail2ban logs not showing at ispconfig logfiles.
until yesterday rkhunter log was showing. i don't remember fail2ban to ever showed there...
Could you help?
I run ispconfig on centos 6.2 and nginx. Yesterday i did a yum update if that could help.