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OK, I think I know what is going on. The duplicate format problem is definitely related to the length of the book title and/or filename. I just added new versions of several books and only got duplicates of the ones with long file names. Books with short titles don't show the problem. Here are steps to replicate the problem:
1. Pick an epub book with a long title (not sure how long it has to be, so I suggest 36+ characters). The epub must have been added to Calibre before Calibre 1.0.
2. Copy the .epub file at the OS level to a flash drive and make whatever changes you want to it. (I use Sigil, but I have no idea if this contributes to the problem or not. I doubt it.) I also am not sure if file size has anything to do with the problem, so I suggest making enough changes to affect the size of the file.
3. Open Calibre (upgraded to 1.0), select the epub, and click on the Edit Metadata button. (Make sure your preferences for adding books are set to "overwrite existing duplicate formats.")
4. Add the new version of the edited epub by clicking on the red rectangle with the white plus sign, finding the file on the flash drive, and double-clicking it.
5. Go to the directory where Calibre stores books and find the book you just added. You should (I hope) find two epubs with similar names. Only one of these (the correct one, thank goodness) shows up in Calibre. The old version is still in the directory, orphaned.
I hope this helps. (Using Windows 7, 64-bit.)
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