If you posted some code to show how you're using the system call -- maybe even try it on some basic task that's similar to the real one, but would be meaningful to us (e.g. "system('ls')" or some such), then we might be able to pinpoint something if you've got it wrong.

Short of that, we have to guess or ask about what you're doing. My first guess/question would be that perhaps the perl script is running with a different PATH, and can't find your C program. Try printing out "$ENV{PATH}", or simply specify the full path to the program in the system call.

Beyond that, I'm not sure what to guess...