For consolidation's sake.

I know the feeling.

I'm pretty sure it would be a bootloader problem, in which case running either fixmbr, fdisk /mbr or fixboot would be what I'd recommend (they are different, but neither work very often ). Does the problem go away if you unplug the 98 drive?

It's unlikely that installing GRUB will help, since GRUB can't actually boot Windows - it just boots the Windows bootloader NTLDR.

If they are IDE drives on the same cable, try reversing the order in which they are plugged.