Are you dual-booting off the same harddrive?
Here's how I got my dual boot system working.
I have a 30 gig HD. Using DOS FDISK I partitioned this into 2 15 gig parts and formatted them both FAT32. I then installed Win98 to first 15 gig partition. Then I stuck my Linux Slackware CD into my BOOTABLE cd-rw and rebooted and installed Linux to the 2nd partition. Of course formatting and partitioning the second 15 gig partition with Linux Fdisk. Now I can boot into either win98 or Linux on start-up using Lilo.
hope this helps