Well it turns out I mirrored the connection header for the Genesis cartridge in my original design. This has caused some issues that should have been resolved by remapping pins in the CPLD, but things failed to work. The USB issue I have been having the past few months that I thought was a hardware issue, turned out to be a software issue after all. I had the description in the USB header info to long that was allowed. Some how it made things work, but not for very long. I am able to write to the NOR Flash and read back the information correctly now. I hope to have the board redesigned in the next few days seeing how I have some time off from work do to the holidays.