You haven't given enough details to be sure, but it sounds like you're running under mod_perl. mod_perl makes a persistent Perl interpreter per child httpd process and things get loaded once (more or less) at child start time. Then again that's why you use it (in production you bypass all that startup overhead after the first request).

There are things like Apache::StatINC (but that's for mod_perl 1; I can't recall what the mp2 one is called) for making changes visible immediately at the cost of a few more system calls each request; that may be what you're interested in. Alternately if you're writing a CGI that's eventually going to run under Apache::Registry (or whatever the mp2 analogue is), configure things to run it as a real run-and-exit CGi during development and testing.