http://www.gnu.org/software/grub/ Grub is nice, there are windows installers for it. But it is mainly associated with linux. You can do some REALLY cool stuff with it (like network boots, etc)
Look arround (google!) the "boot.ini" file, this is what controls that windows bootloader, somehow this probly got messed up, and you can re-write some of it.
quick goggle search revealed this:
http://hacks.oreilly.com/pub/h/2337<oss fanboy rant>
edit 2: it looks like grub/lilo just chain load the windows boot loader, cause M$ doesn't like to support other os-es </oss fanboy rant>
but yeah, so fix your boot ini file, if you are using grub (kinda hinted at first post) that shouldn't matter, as grub just hands it over to the win bootloader, and that looks at the boot.ini, so there is your problem to fix