I agree with what sundialsvc4 said but I'd add a few things:

• When things start breaking and you start down the merry path of fact-finding don't do it with blinders on. When you see other problems with the code flag them as well. An ounce of preventative maintenance is worth a pound of cure and please tell me that you are using some kind of software versioning system before you do anything...even just look...
• While you are at it, why not take a few scripts down the the bare fetch/update/whatever you are doing with the DB and run some benchmarks? You may find that switching to DBI saves clock cycles and works better (or not).
• Looks to me like some incremental rewriting of your code is probably in order anyway. You could move things to packages for one thing instead of requiring .pl files methinks.