I'm not sure if the problem was there before the 2004 update, I never really paid much attention to it until I became aware of the recent issue with the defrag/TRIM system.
After a reboot it did say that the drive was 0% fragmented, so I supposed that was a good sign.
It passed chkdsk fine, that's the first thing I checked to make sure there was no corruption on the drive!
I have a dual boot system, with Windows 10 and Windows XP, and I've tried running the Windows XP defragger on the drive, and it said it was still quite fragmented, so I guess the Windows 10 one didn't actually do its job.
The Windows XP defragger is now defragmenting it (taking ages) and when it's finished I will try running the Windows 10 one again to see if the result is any different now the drive should actually be defragmented.
Thanks, Dave.