You say one working windows, we don't know the history here or at least I don't
Sounds like you Installed Windows NT/ 2K or XP on top of Win 9X installation and later decided to format a partition/ drive other than your C: for a fresh install! (again we don't know details here, just assuming but primary/ active partition any way)
The Boot.ini is not detecting anything just trying to do its job as a boot manager in which case the corrupted or none existing, will just produce errors.
What version of Windows do you now have?
The man with the master plan and dbwillis's suggestion will both work if you have any flavour of NT installed, if you have 9X installed you can just simply delete the boot.ini alongside NTLoader and NTDetect.com safely.
(DanTMWTMP, why can't he just edit the file in Winblows other than the possibility of past multiple NT installs using NTFS with Win9X the only working OS now and the NTFS not being accessible)
How many partitions you have/ had and how you installed your OSs b4 and on which partitions/ drives in what order, would've made helping you easier
I would get my data and start fresh, sounds a bit messy in there!
Good Luck and happy computing!