i have a similar set up to you, win XP and FC2, i found that when i re-installed XP that it wiped over the MBR and completly ignored linux, there is a guide in the tutorial section on setting up the windows boot loader for duel booting, i found this was the only way to stop windows hideing linux from me!!
And as for what boot loader I am running, it is GRUB. I do not want the system to boot into XP by default. I want FC4 to boot by default. But what I am worried about is that if I reinstall XP, XP will change that and make itself the default OS. Then I may not be able to boot into FC4 at all. So... Thank you again for your help.