I've used Perl in a service and called from services quite a bit now (mostly using the Perl Dev Kit from ActiveState). So here are some questions that might help me/us help you!

Are you receiving any errors?
Is anything being written to the Event Log?
Are you using the Perl Dev Kit -- PerlSvc (I have a whole other list of questions, if so)?
As mentioned in an above post, are you giving full path to modules (Windows paths are notorious for not working)?
Are the modules using other modules that may not be in your path?
Is Perl associated with .pl files? If not, are you calling the script with perl <full_path>\<script_name>?

If I think of any more, I will post here again. Good luck!