I just discovered that this patch existed this morning, and it solved a two week long headache. Just wanted to share.....

From the MS Support description
The Windows IDE Hard Drive Cache Package provides a workaround to a recently identified issue with computers that have the combination of Integrated Drive Electronics (IDE) hard disk drives with large caches and newer/faster processors. Computers with this combination may risk losing data if the hard disk shuts down before it can preserve the data in its cache.
I have been trying to solve a shutdown - reboot issues on our 1 Ghz machines for a while. This solved it instantly. Seems that data loss will sometimes corrupt the registry. They all have 7200rpm ATA66 drives with 98SE and 2mb Drive cache.