If you analyse the drive again, do you still have lots of red blocks? Also how many files (roughly) are listed in the file list.
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MrRon
When I originally installed Defraggler, I was very pleased (so much so, I prematurely sent a donation). It appeared to be doing a great job. Unfortunately, having processed a few more devices, I'm simply mystified as to the inconsistent and seemingly ill-considered protocols. To highlight this, I'll use one test case which leaves no room for doubt: I have a 160GB USB drive formatted NTFS. There is 66GB in use, slightly more than one third of the total. Probably 20 of the files are 1GB or more. Given this scenario, it should be possible to defrag every single file. I could defrag the drive simply by copying all 66GB onto another drive, erasing it, and then copying the files back one by one (caveat, some copy programs might needlessly interfere in that process, leaving some fragments). However, after running a basic pass, I ended up with about 50 fragmented files and a little over 1000 fragments.
So, I set the options to force files 250MB or larger to the end of the disk. That seemed to reduce the number of fragments a little bit, but at the end, the graphic display showed what appeared to be the end of the disk with a solid block of red clusters(?). The number of fragmented files had been reduced by about 10. There was plenty of free space (white?) on the display, so I'm wondering, why didn't it defrag the remaining files?
Next, I reduced the limit on the 'move to end of disk' to 25MB. Since I had already moved the 250MB+ files to the end of the disk, I would have assumed that Defraggler would leave them where they were, and simply add new ones where it left off packing the first group. Instead, it appeared to refragment the first set of files in order to move the smaller files into their place. This sounds absurd to me.
UPDATE: After some investigation, I find that the NTFS file system design is (predictably, since it's a product of Microsoft) seriously flawed. Clearly, using a large USB external device (or any large drive for that matter) creates major conflicts if one were to attempt to store (lets say for example): one branch containing lots of files, many small documents, images etc., along with some number of large multimedia files, DVD ISOs, or ZIP archives. In the above test case, I find that my 'MFT' has 18 fragments, which 'cannot be defragmented' (according to the Microsoft documentation). This is absurd, hence explaining the absurd results referenced above. Apologies to Piriform for the inuendo that they might be responsible.
FYI, I plan to navigate around this problem by re-formatting all my NTFS external media with at least one virtual drive (either ISODisk or TrueCrypt at the moment) which should have the effect of reserving a large contiguous 'super-cluster' which can be used either for big multimedia/zip files, or lots of little files, while not overloading the brilliantly conceived Master File Table (which can't be resized, moved or defragmented).
(I can only say thank God for the European Union's legal team for going after this criminal organization (stock symbol:MSFT) which has fed off the Personal Computer industry almost since it's inception.)