Perl on its own doesn't cache that I know of (assuming you didn't add specific cacing routines into the program, or use an alternate perl context)-- but some disk drives will. Sometimes it's the individual disk drive, sometimes it's an optimization of the OS. (laptops are much more likely to use disk caching, as it can improve battery life)

Try changing a couple of the files, re-running the program, and making sure that the changes were picked up -- if they were, I wouldn't worry about it.