Just registered to say that I am having similar problems. I have used CCleaner for a long time now and so trusted Piriform to make a good defrag program. However, after 48 hours, I'm sitting at 25% complete and in the last 12 hours it has only increased by 1%. Fragmentation is 52%, just like it has been throughout the whole process.
My system is running Vista Home Premium 64 bit, my HD is 1 Terrabyte (with 300 GB used). For Kas' information, the machine is not Valve driven, nor is it Russian . It is, in fact, only 3 months old, has 12GB of RAM and is the fastest machine that I could afford back when I bought it. It runs every other program that I have asked it to at lightning fast speeds.
I have only just found out (by reading this thread) that the system restore points may be responsible so I will try disabling them. However, so far, Defraggler falls a long way short of what I hoped it would, which is a shame.