I ran into this same issue with pair.com when running Greymatter or MT. They suggested calling the CGIs through their CGI wrapper. It is detailed at http://www.pair.com/pair/support/library/s...gi/cgiwrap.html .
This runs the CGI under your user id rather than the nobody account, and supposedly allows more memory usage per script. All you would have to do is initially link to the message board as http://www.movabletype.org/
cgi-sys/cgiwrap/accountnamehere/cgi-bin/ikonboard.cgi instead of what you have now. This would mean moving the cgi to the cgi-bin because of security reasons.
Before I switched to running through this buffer, Greymatter would choke half way through rebuilding everything with internal server errors. Now it works fine. Hope that helps!