ikonBoard really doesn't play nice with mod_perl. There's an attempt to support it, but it's not there yet. I just pulled down v3.11 this week to evaluate it, and I still haven't gotten it to run properly under mod_perl.
It runs great as a cgi app though. If anyone wants to try to hack it to make it run better under mod_perl, I'd suggest installing it asa cgi app first. If you don't, the installer doesn't support mod_perl at all. You'll have to touch installer.(cgi|pl) after each step so it recompiles and runs properly.
Code appears to be written well... great functionality as a cgi, but mod_perl support just isn't there yet.