I've noticed that when I defrag my PC using the built-in Windows ME defrag utility, there is still a residual ~10% fragmentation rate.
I don't really know how accurate Pc PitSpot is, but that kinda result doesn't surprise me. Some people run defrag twice because of that. Not a bad idea if you know your hard drive is badly fragmented; for example after deleting or uninstalling lots of large files, applications et al, or when performance is terrible.
Altho I think 10% is high, I usually defrag before I'm that fragmented.
So I'd probably defrag twice and start defragging more often in the future.
Could it be that this '"background fragmentation" is set to be so on purpose so as to allow for smoother functioning of the PC?
Don't think so.
Your Pc would run best with no fragmentation at all. Defrag will have a harder time if your Hard Drive is about full. The same is true for windows in general. If it is too full things will actually quit working.
Or is this some weakness in the Windows defragmentation utility?
Some third party defrag utilities claim to do a better job, run quicker et al. I've never tried any so I can't recommend a good replacement. But I doubt any would achieve perfect results on your typical computer. Some probably do a better job than windows. But I don't know if I would call it a weakness in the Windows utility. that would be some tricky code to write and they probably did as good of job as they could.
The next time you defrag try running ScanDisk in Ms-dos mode and do a full surface scan, and then run defrag twice (best in safe mode) and then test it at Pc Pitstop and see if this helps lower the percentage.
Hope this clears things up some.