Warning! Probably not the solution. I've had this problem before and I don't think it's a DOS/UNIX test problem. (Some years ago at a different company.)
However, see if the program operate differently if you type
$ perl program.pl
$ program.pl
With 5.6 on redhat 6.2 a Dos newline will run example #1, but not #2. (bash command not found)
Back to the problem
It might be a system problem. Check your inode space. Do a df -i. I don't think that's the case, but some other system resource is hanging you up.
The previous posts give good clues as well. Is this a program that performs writes? I know I ran into this problem before and it was most likely with a program that opened multiple files and wrote out log files. This problem is really bugging me that I don't remember the solution.
Hopefully this will give you an area in which to look.

UPDATE: Another idea. Are you using Samba or maybe NFS? For some reason that's tickling the back of my brain.

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