I think I may have found the problem...
The Hauppauge TV card seems to have either buggy drivers or the capacitors (the infamous electrolytic SMD type of capacitors) on the card are affecting ONLY Windows 98. Once I installed them, the system started acting up, and a registry recovery didn't help. First sign of problems was a shutdown that hung, like I have seen before, but then when I tried installing Quicktime 6.52, the installer glitched out and took the system with it. So much so that I needed to reinstall the OS. Luckily I discovered Clonezilla, and have two recovery images (one "start from scratch", one updated at base level) on a USB drive, so now I shouldn't have any problems. I also stopped using the July 2007 Auto-Patcher program (instead using the Unofficial Service Pack 3 update from MajorGeeks), and that seems to have calmed things down. The system seems to run much more smoothly and faster.
My ATI card also seems to be on its way. I'll see if the problems come back when I install it, based on a previous topic I posted a month or two ago.
EDIT: I am still getting that odd 540MB (Windows sees 528MB) memory count when I restart the system, though. Maybe its the BIOS?
EDIT 2: Huh. I guess the BIOS has some kind of trouble with any more than 512MB when it restarts. It really doesn't matter in the grand scheme of things, because none of my games use more than 512MB anyways. I'll try the 1013 BIOS later.