So I ended up with a nasty virus that broke the boot loader for windows.
After several attempts to restore the system (and almost throwing the computer in the street) I remembered that I had a copy of Kubuntu. So I did a clean install on my 2nd hard drive, backed up all my files on a 3rd drive and was going to do a clean install of Vista. So I restarted my putter and went to the boot menu, I changed my mind and was going to explore Kubuntu some more and the putter asked me what os to load and so I tried Vista and ta da it worked.
So I said all that to say that I am using ubuntu's boot loader to load window.
I would love to here if anyone has run into a similar problem.

Hm... sounds like very classic case - using Linux bootloader to boot OS (in this case only one - windows).
It's not a problem, really. If you don't have any issues you may leave it as it is now. If you don't like it this way - well, can't say for Vista, but on XP one have that nice "Rescue mode" when booting from the Windows' install CD. For exact instructions you may search in Google for "fix mbr". There you could also find some fixmbr utility to fix your Master Boot record (MBR) and not worry about that Kubuntu's loader.