I'm using v1.03 and I've installed this version on two computers. The first one takes a very long time to defrag (HD capacity: 146 GB) while the second computer takes normal time (HD: 25 GB).
I hope you'll find the bug / reason for this behaviour soon.
System: XP SP3 and all updates installed
//EDIT: I've added the debug file
Defraggler.exe._1_3_93__2008_10_06_18_45_.zip
Defraggler.exe._1_3_93__2008_10_06_18_45_.zip