The shadow copy system will use space. If enabled, each time you save something Vista simply renames the original and hides it. The new file is saved, and the original file becomes the backup. The amount of disk space that shadow copy uses can be determined by the user or completely disabled. I'm not currently on a Vista system so I don't remember where this is, but I'm sure Google will be handy! There could be some other things but I would check that if you haven't already. Cheers!
EDIT: For example, 1GB Photoshop file can quickly become 10GB if you are working for a few hours and save the file 9 times. Windows will keep each version, hidden, until the disk quota is reached for the shadow copy service. More on that here: http://www.microsoft.com/windows/products/windowsvista/features/details/shadowcopy.mspx