Update:
I sent my Nucore usb board out to Don at Big guys and he could not find anything wrong with it. He sent me back his board since he knew it works 100% in his machine. Unfortunately it did not solve my problem with saving the high scores or the time and date. So I might have to try and reload the nucore software next per his advice. I hate to do this as I'm nervous I will screw it up and the result will be a completely dead game. At this point the game works and I would prefer to live with no high scores than no game at all. So this leads me to some more questions for you computer guys...
First question is about motherboards. I searched around a bit and found two old threads where both people were experiencing similar issues with time/date and high score retention. They both had the same motherboard that I have, an MSI GF615M-P33. In one of the threads the solution that ended up fixing the problem was replacing the motherboard with a new one. So my first question is: can I just swap motherboards? Are they plug and play? I would swap the MSI GF615M-P33 with the exact same thing. I assume I'll just need to adjust the bios upon start up and that's it? There are some on ebay for $40. I figure if it fixes the issue, great, if not it's cheap insurance as a backup motherboard just in case I ever do need it.
My second question is about the hard drive. As I stated before I hate to goof up my hard drive trying to reinstalling software and make the game unplayable. So, if I got another hardrive, I could try reinstalling software on the new drive and see if that fixes the problem. If not I could just plug my old one back in and be back to where I'm at now. Am I correct in this thinking? Also, is there a way to copy my existing hard drive to a new hard drive so that I could try reinstalling just the Nucore software without having to worry about the Linux portion?
Any advice is greatly appreciated!