Windows really shouldn’t play into whether or not a disk boots. Generally speaking, when you direct the computer to boot from a disk instead of the hard drive (for windows), the disk is loaded into memory. Windows plays no role in booting from a CD/DVD. Now, while it’s booting, there are all kinds of hardware checks that are going along with the booting process. Given that you were able to get the computer to start booting from the disk, but that you ran into errors during boot, I would think that one of two things are going on. Either the hardware you are trying to boot from the disk is incompatible read, too old, the most likely scenario with windows 98 or defective, or the disk has errors or is scratched to the point of unreadability.