I'm not sure if this is only my problem or not, but vacuuming defs only seems to work when the file is freshly opened/reverted. If I make changes to a file that causes new defs to be created, then delete something else that no longer needs some defs and do a vacuum defs, it does not. If I save the file and then do a vacuum defs, it still does not. Only if I reopen and then vacuum or save then revert then vacuum does it seem to work. It's not too big of a deal, but the file size is reduced a little when the unused defs are no longer there, and I normally do this before saving without thinking about saving, reverting, vacuuming, and then saving again.
I'm on XP SP2, and this seems to be the case with 0.45 and a development snapshot I've recently downloaded.
Brian Vanderburg II