Beyond making sure that Perl itself is accepted as an executable in IIS6's new script restriction area (I can't get to our local IIS6 box at the moment to dig up exact instructions), you should make sure that the directory as mapped in IIS has script execution permission, and that the IUSR_ account for the machine has execute rights on the files.
After you get things working, please upgrade. <img src="https://www.ubbcentral.com/boards/images/graemlins/smile.gif" alt="" />