HEY! Got the server working by putting some of Thread::Queue into my code, and now it seems to be running like a champ. If you'd like to see the code let me know, but I'm guessing you have a fair idea of how its working. Ran 200k commands in 2 hours without a hiccup.
And that is really interesting that threads got messed up. I'll definitely try downgrading perl and testing it out but as it is no longer a time critical thing, and more a matter of interest, I probably wont get to it until next week.
Again, I really cannot stress enough how thankful I am for all your help debugging. Could not have gotten this far without you.