How are your drives configured: Are both set as masters on separate channels, or is one master and one slave on the same channel? I run two separate drives, one master and one slave on the same channel. I have Linux on the master drive and Windows 98 on the slave and dual booting works fine. I did have to edit the file in /boot/grub/menu.lst, which is the list of options you have when starting the computer. As you can see, I have two Mepis kernels on the first drive, and Windows on the second. The trick to making it work this way is mapping the second drive so that Windows THINKS it is on the first drive:
default saved
timeout 15
color cyan/blue white/blue
foreground ffffff
background 2f5178
splashimage /boot/grub/mepis.xpm.gz
title MEPIS at hda1, kernel 2.6.7
kernel (hd0,0)/boot/vmlinuz-2.6.7 root=/dev/hda1 nomce psmouse.proto=imps quiet splash=verbose vga=791
initrd (hd0,0)/boot/initrd.mepis
savedefault
title MEPIS at hda1, kernel 2.4.26
kernel (hd0,0)/boot/vmlinuz-2.4.26 root=/dev/hda1 nomce quiet splash=verbose vga=791 hdc=ide-scsi hdd=ide-scsi
initrd (hd0,0)/boot/initrd.mepis
savedefault
title Windows 98SE at hdb1
rootnoverify (hd1,0)
map (hd0) (hd1)
map (hd1) (hd0)
makeactive
chainloader +1
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