Well it's obvious from the code you've posted where the error is.

Erm, well aside from that in all likelihood your former CGI was dependent on variables being cleared when it exited. Under mod_perl they're persisting between invocations so you're seeing data accumulated over several runs. The mod_perl guide discusses how to port CGIs to mod_perl, and you may want to check out Apache::PerlRun (or it's mod_perl2 analogue; which I can't remember the name of since I haven't touched mod_perl in aeons); that module is a bit more agressive than Apache::Registry in clearing things out making a more CGI-like environment (at the cost of more overhead each request, of course).