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Windows 98 is slower because of all the extra overhead. That is, the active desktop, integrated web browser, and visual effects. I have always noticed that NT runs better than Win 9x because NT is a true 32 bit OS. I would suggest disabling the animation effects in windows 98, use FAT32, and defrag your harddisk. Also, check your start up folder to see if apps that you don't use are being loaded.
PS: I hope you have a lot of ram on that 98 installation too.