I don't play too much else besides Freespace. Besides, anything else I play, I play under my XP partition, rather than my Win98 partition, which I use almost exclusively for FS. Also, the other games I play, didn't have any probs with my on-board card. As for formatting, the last time I had to reformat was almost a year ago. Long story:
My older system (pre-upgrade) used 30GB IBM drive, added 120GB WDC, moved most of my data to the 120GB. IBM drive failed, installed OS (WinME) onto 120GB drive and played from there. That OS failed a few months later, had my GF's kid brother split my drive into 2 partitions, one for my data and primary for the OS, which was now Win98SE that he gave me. Had problems where FS ran too slow, eventually turned out he'd forgot to install AGP drivers, so my VC was behaving like a PCI card. I added 'em back myself and got the performance back. Then upgraded CPU, MB, VC, & RAM, switching to the on-board sound & LAN, and he added a 3rd partition for WinXP. Unfortnately, he lost my data partition in the process. Because of file allocation system, only XP can detect all partitions, but Win98SE partition can only detect itself. Last format from Win98's point of view was back after my WinME failed.
I will give that new build you posted a try, Coolmon. If that fails, more drastic action may be necessary.
Later!