Go Back could have been the problem.
I would think that maybe your XP installation is OK. The non-recognition of the second drive is because XP won't recognize the EXT3 files sytem.
I would recommend using the Recovery Consol proved on the XP disk. If you have an XP book, learn the commands and you can repair the MBR for XP. This will overwrite the old MBR and destry the GRUB (no big deal)...but make sure that you have a Linux bood diskette handy). After the Sys.ini files and MBR are working in XP...see that it works. Then boot into Linux and re-install GRUB. I'm not sure where BoBack would fit into this picture at this point. You would probably have to re-install that too.
The only other option, I would think, would be to start over, but if you can get into your disk with DOS or some other way of seeing your important data, get those safe first.
I have installed RH9 on SEVERAL machines, also re-installed several times on different partitions and disks on WinXP and Win2000 machines and never had a problem with corruption of the boot sector for WinXP. That's why I think that you are onto something with GO back. Also i am in agreement that you should check your jumpers. However, after checking the Jumpers and if you change them, then you definitely will have a WinXP boot problem until you rebuild a MBR or re-install.