So I have a few Win98SE machines, including a P3 600 Slot 1 440BX and a P3 1ghz Coppermine on an i815EP board (Intel D815EEA). Both of these exhibit the same issue - on a clean install, after installing chipset drivers, when DMA is enabled for the primary hard drive (spinning rust) the shutdown process seems to cut the power a few milliseconds too soon. This means it doesn't always finish flushing caches and doesn't mark the drive as clean. Scandisk runs on the next boot. msconfig->General->Advanced->Disable Fast Shutdown does not by itself help.

I found only one workaround that allows me to keep ACPI and DMA enabled - I marked the primary OS drive as "removable" in device manager. This has some side effects where applications may not allow running on what it thinks is removable media. I think most folks that run into this issue either disable ACPI, DMA, or just ignores/disables scandisk. There's something about marking the drive as removable that changes the cache flushing behavior (even with write behind caches enabled for removable media). Maybe it just changes the order of operations, flushing removable media first, then running the rest of the shutdown process.

Anyone have thoughts on this?