If you want to take a chance, you could do this:
Delete the Partion(s)
Format (Through Windows install. Just turn the computer off when it's done.)
If you didn't write too much data you can use a program like TestDisk to recover the old Windows partition.
If that doesn't work.
You can delete the partition, install Windows. Then take the drive to another installation of Windows somewhere (or some other OS that has this) use a Virtual Partition program. It'll allow you to Grab all the data.
You were on the IRC channel earlier, and you mentioned you had Linux on there too. As far as I know you'll have to whipe it all, since Windows is anal about partitions. (You have to install Linux after you install Windows)
I just had a problem of a fragmented MFT ... s**tty situation. At the time, I didn't know about some of the 3rd party boot defrag programs.
But you could also have a corrupted registry. That should be recoverable with some of the types of tools I've mentioned.
But, yeah, formating, then recovering might be the best option ...
Try backing everything up when you get it all back up and running onto a DVD or something like that.
[Edit]
I should mention, you can check all of these things ... shouldn't have done all the reinstall stuff yet though.
Anyway, slap the drive in another bootable computer, goto the drive and then defrag, do an analasys and view the report, check out the Fragmentation of the MFT. (There will be some, but there shouldn't be too many)
That could be one problem.
You can get that program I mentioned, TestDisk (it's free just search google for it)
Make a boot disk (A drive -> Format, check "MS-DOS Boot Disk) Then copy over the testdisk.exe to the floppy. Restart and run it.
Analyse the drive (Find some documentation online)
You're basically looking to see if the MBR is the same as the MBR backup.
I can't remember a program to check for partition table corruption ... but you can check with a hex editor ...
There's also the possibility of Registry Corruption ... and I don't remember how to check for that.
But that's what Google is for.
Oh yeah. This site might help:
http://ntfs.com/
Blame it on Microsoft, God does.