This doesn't have anything to do with disk free space. Rather, Diskeeper simply aims to improve performance, rather than striving for 100 percent defragmentation. The philosophy works. I read this in PC Magazine's 12th annual utility guide. Diskeeper, although it doesn't defrag 100%, the performance gains gotten by it are as significant as performance gains accomplished by other defraggers. I had the exact same thing happen to me when I ran Diskeeper, though it was closer to 50%. If you really want 100% defragmentation, PC Magazine also recommended Raxco PerfectDisk 6.0. I haven't used it; I'm just saying what PC Mag reccommended. All in all I guess I wouldn't worry too much about it, if that's their strategy and if it seems to works as good as others.