Download Microsoft Xna Game Studio 3.1
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Are you sure its the 3.1 because for some reason at first mine installed the 4.0 even though I clicked on the link for 3.1.
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Turn everything off and leave it off for at least ten minutes. Then turn it back on. Repeat if necessary.
Try a clean boot on those programs and re-download it. I had a similar problem and a clean boot helps it, its like a roundhouse kick from Chuck Norris. I have don this on 32 and 64 bits so thats not the problem. Try downloading from the two links, I forgot which one I used but are working.
I'm sure it needs 3.1 since it was updated for the ZuneHD
http://www.zuneclan.com/zune-applications.php
http://visualboyzune.com/tiki-index.php?page=Install
If anything you probably didn't extract the file.