I am not sure if this happens since the 2.09 release only.
But this is a definitly a bug which should be fixed - i've never seen a defrag application which is cpu-bound instead of io-bound.
I'm also having the same problem with the most recent release of defraggler - are there any news on this? Defraggler estimates "> 1 day" for defragmentation (on a 500 GB drive)....