I'm no expert, but I'll offer my opinion.
You cited that your system uses 98SE. From this I assume this is just an extra computer and you have the vast majority of your work and software on another computer.
If this computer is dedicated to your AI interests, how difficult would it be to backup your data, reformat the hard drive, and reload your 98SE OS, the drivers, and your AI software?
Starting from scratch and cleaning up your system installation might save you considerable time; if you have 98SE and driver (motherboard, modems,...) disks readily available.
Additionally, this should increase the processing speeds of your AI software.
Be sure you know where all of your brain building data resides so you don't accidentally delete it; I can't help you there.
If you still have a problem following this procedure, then you know the problem is in the AI software you are loading and its' compatibility with your version of 98SE and/or your motherboard. At least then you won't tend to be fighting an endless battle.
James