With XP, we do the first bit where you are asked if you want to format the drive, and we say yes...and it does it's thing for what seems like forever, then it says re- boot. When we do it says would you like to format this hard drive?
This is a bit of an aside, apologies Rod. There's a utility that works pretty well for reading NTFS hard drives. But you have to copy some XP files over to 98 before you can use it... So probably not helpful for you... Also don't use it to copy big files, unless you have to! It's deadly slow doing big files.
Back to the subject at hand -- how does Windoze know what to do after reboot? Does it store some BIOS parameter or something? If so... maybe a battery issue? I don't know, I'm just guessing -- shoot me down if it sounds dumb!