This thread in another forum seems to discuss exactly this same issue
You need to skip past a massive amount of info quoted from files on the problem system.
Even though the thread says grub2, it looks to me like a grub answer. Maybe grub2 is less different from grub than I understand.
It says to add an entry like this to your /boot/grub/menu.lst file
map (hd0) (hd1)
map (hd1) (hd0)
The two map commands reverse the drive identities (lasts until the computer is rebooted) as I described above.
The root command selects the partition you will boot from.
savedefault says that once you make this choice, if you later let the menu timeout, this will be the default choice. You might or might not want that behavior.
makeactive marks the partition with the boot flag. That does neither harm nor good in your case. But if you were multi booting more than one OS that cares about the boot flag, that line would be needed. Windows cares, Linux doesn't, so you can leave the Windows partition always marked bootable.