"Does nothing" isn't terribly specific. Does it compile? Does it throw an exception? Does it run but not do what you expect? If so, what DO you expect, and what - EXACTLY - did it print?
Do you know the perl script works? Can you call a simpler perl script and see if that works - something that would have a result you can see, like touching a file?
I have never called perl from java (or java from perl). I do know there are some caveats with using the process builder, but i've never really paid much attention. I'm sure if you search the various forums here you can find someone who has linked to it.
There are only two hard things in computer science: cache invalidation, naming things, and off-by-one errors