Oh sorry guys, I figured it out.
It wasn't the root file system but a hard disk installation of Knoppix Linux on a different partition that was dirty. I guess because it wasn't the root file system, Slack didn't try to fix it. I booted the computer into Knoppix and everything got fixed and stayed that way. I imagine I also could have run fsck manually and did the same thing.
So now I'm just playing around with some of the new stuff in Slack 9.1. Which includes epiphany and the new XFCE (I already miss the fast, simple, and clean file manager they had in the previous versions, but maybe I'll get over it).
It's nice to have Alsa sound installed by default. Somehow, it always sounds better on this ymfpci sound card than the OSS driver did, I don't know why.
Overall, Slack 9.1 seems to be doing fine on this machine, which is saying something because it is actually very sick hardware that won't even install a recent MS OS! (Which is why I got it for free in the first place)
Oh yea, and if this was any sort of mission critical machine, I certainly would use a journaled file system. Since this is mostly a test/backup machine, I am just going for the lowest common denominator (well, that isn't FAT anyway) that is compatible with most anything I might boot on this thing.