Hi there,
I've noticed that Defraggler won't defrag some files despite them being fragmented. Through investigation, I found that Defraggler reads the MFT of the drive first and then begins defragmenting which leads me to believe that you're manually parsing the MFT (which is fine - and fast).
However, the files that remain fragmented tend to be the ones where the DATA attribute of the file is in an attribute list (and thus exists in another MFT entry) - it doesn't seem like Defraggler is parsing this correctly.
I suggest (given my assumptions are correct) that Defraggler be extended so that it can parse these attributes and better detect when files are fragmented.
Regards,
Mike