I had a similer thing the other day, i replaced my C drive with a 10,000rpm one. went to format the old c drive and it wouldnt let me due to "files in use".
so fine, i used ntfs4dos, got into dos and deleted the entire contents from there, back into windows and it still wouldnt let me format due to "files in use" and reported that it was about 5 gig used. the drive looked empty.
Back into dos i hit the old "del *.*" and it removed two files.. that i couldnt see even in dos.. strange.
The now completely empty drive then formatted fine.
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