Boot problems after new hardware!

I recently added a new CD burner to my second IDE channel. Previously I
had my hard drive as the master device on ch1 whilst my CD-ROM was the
master on ch2.
I discovered that the only way I could add my new drive was as slave to
the CD-ROM on ch2, as any other combination lead to the boot process hanging
halfway through.
I'd taken care to use the correct cable plugs & jumper settings on the
back of the drives & from what I've read about hardware installation I can't
see why, as long as the jumpers are correct, I can't set up the IDE devices
as I please?
Is there some BIOS setting that I should investigate to set up new IDE
configurations & what is the most likekly cause of the faliure to boot W98
in any other config other than just adding the new device to a free space?
Thanks in advance for any suggestions!