could be errors on the disk. id run some disk scans on it. how old is the drive?
edit: while the above is true wouldn't it at least show up on the system disk size?
you can adjust the length of time windows will save restore points. i'd recommend 2 weeks at most.
if you don't have a disk scan there is one built into windows, type cmd into the search box or run box on your start menu and hit enter. a black window should appear, then type in chkdisk and hit enter. while this is running I recommend closing everything, and going away for 20 minutes.
also you might want to look into ccleaner.
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