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#190
The defragger organizes your HD's while a boot time defrag is able to organize System files as well, which would be running otherwise if defragged from the OS.
I have only defragged OS HD's and not data drives. Someone else will need to advise you on the efficacy of that.
If there are file system problems then run a full Disk Check.
If problems persist test the HD with the maker's HD Diagnostic extended CD scan.