Did you have saved server configuration ?

It sounds as if before you had a CGI setup (execute foo.pl), but it sounds like you're running under a persistent perl process under FastCGI or PerlEx , but your programs can't cope with the change

See CGI to mod_perl Porting. mod_perl Coding guidelines, Lexical scoping like a fox, Variable Scoping in Perl: the basics, Mini-Tutorial: Perl's Memory Management

I'm also sure the IIS/FastCGI/PerlEx ... docs have a FAQ section for this but I don't have a link handy