I think you'll need to post your code, if that's possible.  Otherwise, there are so many reasons it could be failing.  Is it small enough of a program that you can post it here?  If not, can you trim it down in size to the point that you can?

In the absence of seeing what you've written, there are a few things which come to mind:

• Are you running out of processes somehow?  Check with ps
• Is the system command failing at some point?  Check by printing out the exit value from the system call; it's saved to the special variable $?.  In fact, if you haven't done so already, try reading about the system function with:  perldoc -i system.
• Are you able to "run the string outside of the perl script" even after it has started failing from within Perl?  

But these are just thoughts ... I think once you post an actual example of the code, and especially if it's something that can be duplicated by one of the others here, you'll likely be pleased with how quickly we can help you detect the problem.