Open an output file to the STDERR filehandle, and pepper your code with print STDERR "\$thisvar=($thisvar)\n"; statements to test whatever assumptions you're making about the programs state at various stages throughout the execution. ...of course I don't mean literally "$thisvar", use variable names that you think you know what they contain. Verify that they do. Also use the same technique to verify that you've arrived at logic branches you expected to arrive at, or that you've looped where you expected to loop.

Then review the log file. If your testing of assertions and expectations is thorough enough, you'll find exactly where the problem is. If I were to debug your code, and if the issue weren't immediately apparent, I would do the same thing. If you run into trouble during this process, let us know where you're hung up.