One of the most essential features any defragging program should have is a "Boot Time Defrag" option. Regardless of whether it is a free program or purchased.
Boot Time Defrag does a much better job of rearranging the files, folders, etc. prior to the Windows startup programs so all pieces can be effectively defragmented.
The analytical processes of a defrag program are a little different from one to the other, but essentially they get the job done. That's why one program may state 1.2% defragmentation while another states .80% defragmentation.
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I could understand a few small bits that may have moved between times. However after completely working the second have of my data on the second pass, Defraggler has left me wondering why this was not done on the first pass and that defragging may never be completely finished at that rate.
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Many free programs are not able to do a complete defrag on the first pass, even Diskeeper in it's early days could not do it. PerfectDisk was one of the first to be able to do it effectively.
Now a lot are doing a complete thorough defrag on the first pass. If it's the first time the program is run it will take some time to do it, subsequent passes being faster.