Without a cut-down and running code example of your problem, we can only guess.

If you'd ask me for a blind guess, I'd suggest to prepend/append an echo redirected to a file to the command being executed - funny filenames can have interesting effects. Secondly, your print statement after system() might indeed execute but get buffered (instead of being flushed) while your script hangs _after_ returning from system().

For debugging, consider something like warn("system returned with output: ...\n") if $o_debug. For further ideas, consider Debugging and Optimization