Well, run Scandisk, make sure everything is registering as being there.
Have you emptied your recycle bin lately? Stuff in there still counts towards disk free space.
Also, you should realize that a drive adverised as 40 gigs really only has, what, 37.5 gigs, or something like that.
Other than that, basically you just want to look closely and make sure there isn't some folder off somewhere with 5gb of junk. Frequent offenders here are temporary internet files, windows/temp and 'my shared folder' or wherever a P2P client downloads to.
I assumed you're using Windows, sorry if that isn't the case.
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