Based on the feedback on the UBBThreads site, this seems to have been the intent. They would exploit one board, and then get a script into the system that could add the iframe to every php and html file found on the server. While the exploit didn't happen on the empeg board, it was affected alongside many other files on the server. Thankfully Vito caught this really quick and had Apache turned off in less then 15 minutes.

I'd also like to thank Vito for the cleanup script he wrote. With a quick bit of python, he had every file on the server cleaned up pretty quickly.