Yep - in this case it's a string passed to the shell, so the shell problem does come into play so I'll have a look at that angle in a little more detail.

Unfortunately I'm running out of ideas. I think it would be useful if you could show us a bit more. Though I understand that if the script is complex enough, a Short, Self-Contained, Correct Example is probably a fair amount of work, but you haven't even shown a rough sketch of what your system call looks like - if it's just a single executable, if there are arguments, variables interpolated into the string, or if there are shell metacharacters can all make a difference. Note that you can force system to avoid the shell and use execvp directly (on *NIX) using the form system {'/path/to/script.pl'} '/path/to/script.pl';. Also, you mention system calls that your subprocess is doing, what kind of system calls are they?