I have a pretty good idea of how files end up getting fragmented. That said, I just copied ~3,200 files of varying sizes (from a few KB to ~20GB) from an external USB HDD to an internal, freshly formatted (under Windows 7 x64), NTFS, 2TB, 5400RPM, WD, SATA, non-system (i.e. secondary) drive, filling it up 57%. Since it should have been very much possible for each file to have been stored in one contiguous block, I expected the drive to be fragmented not more than 1-2% at most after this rather lengthy exercise (unfortunately this older machine doesn't support USB 3.0).

Windows 7's inbuilt defrag utility told me after a quick analysis that the drive was fragmented only 1% or so, which dovetailed neatly with my expectations. However, just out of curiosity I downloaded and ran the latest portable x64 version of Piriform's Defraggler, and was shocked to see the drive being reported as being ~85% fragmented! The portable version of Auslogics Disk Defrag also agreed with Defraggler, and both clearly expected to grind away for ~10 hours to completely defragment the drive.

1) How in blazes could the inbuilt and 3rd party defrag utils disagree so badly? I mean, 10-20% variance is probably understandable, but 1% and 85% are miles apart! This Engineering Windows 7 blog post states:

In Windows XP, any file that is split into more than one piece is considered fragmented. Not so in Windows Vista if the fragments are large enough – the defragmentation algorithm was changed (from Windows XP) to ignore pieces of a file that are larger than 64MB. As a result, defrag in XP and defrag in Vista will report different amounts of fragmentation on a volume. ... [Please read the entire post so the quote is not taken out of context.]

Could it simply be that the 3rd party defrag utils ignore this post-XP change and continue to use analysis algos similar to those XP used?

2) Assuming that the 3rd party utils aren't lying about the real extent of fragmentation (which Windows is downplaying post-XP), how could the files have even got fragmented so badly given they were just copied over afresh to an empty drive?

3) If vastly differing analysis algos explain the yawning gap, which do I believe? I'm no defrag fanatic for sure, but 85% is enough to make me seriously consider spending 10 hours defragging this drive. On the other hand, 1% reported by Windows' own defragger clearly implies that there is no cause for concern and defragging would actually have negative consequences (as per the post). Is Windows' assumption valid and should I just let it be, or will there be any noticeable performance gains after running one of the 3rd party utils for 10 hours straight?

4) I see that out of the box Windows 7 defrag is scheduled to run weekly. Does anyone know whether it defrags every single time, or only if its analysis reveals a fragmentation percentage over a set threshold? If the latter, what is this threshold and can it be changed, maybe via a Registry edit?

Thanks for reading through (my first query on this wonderful site!) and for any helpful replies. Also, if you're answering question #3, please keep in mind that any speed increases post defragging with 3rd party utils vis-à-vis Windows' inbuilt program should not include pre-Vista (preferably pre-Win7) examples. Further, examples of programs that made your system boot faster won't help in this case, since this is a non-system drive (although one that'll still be used daily).