Yes both disks are using fat32, as mentioned above I have tried configuring the 98 disk as slave to the 2k disk and visa versa, the machine refuses to boot, I get primary hard disk falier insert boot disc blah blah blah message.
I have not tried making the 98 disk secondary master , I will give that a try today
I have extra long ribbon cabled on the ide sockets because the cd and h/d sit on top of my desk not in the machine, I could shut down change discs and reboot in a matter of moments, so I have never bothered with dual boot system.