high cpu usage, almost no disk activity

Any ideas why this may be happening?

Windows XP Pro 32-bit w/all updates, Defraggler V2.16.809

One of my 2 cpu cores is pegged at full usage. Task manager reports Defraggler.exe using 50 % of cpu, 78MB ram. Yet my disk LED is barely flashing. Current state 47 fragmented files (7.0MB), Remaining time: 18h 5m

I have 3GB of ram, 2GB of it empty.

Hello zze110 and welcome to the forum. One thing you might try is this: Start Defragger, hit the Analyze button, then click the View Files button. When the list of files appears, hit the button at the top of the Fragments column to sort the files with the most heavily fragmented at the top. Then one by one, starting at the top, tick on each file and defragment them individually. There was one occasion in the past where this helped me to clear a small group of files that were extremely fragmented* and holding up the normal process.

*Between 600 to 1,200 fragments each!

It could also be that your antivirus is scanning any file that df is liking at moving

There is clearly a bug in the algorithm or it is extremely poorly optimised. While there are a large number of files remaining to defrag, Defraggler goes extremely slow with 100% core usage, defragmenting only one small file every 30 seconds or so.

I see the software is now essentially unsupported and discontinued, which sucks because it is the best defragger IMO just with some major bugs / usage issues (being able to do multiple drives at once, even via a second instance, disable sleep while running etc.).

Not sure where you get that it's abandoned or unsupported but I guess you are allowed to have opinions, even if wrong they are.