I am just experiencing the same. In the past I had always been using O&O but recently I decided to not pay money anymore for Defrag software when there's free options.
A few hours ago I started a Defrag on an external USB drive that is 600GB in size, with 280GB used. It's mostly mp3 files, acronis backup files and program installation files.
The point is, it didn't look fragmented at all, all blocks were shown in blue, they were in perfect order, and it said 0% fragmented. I don't know why, but I clicked defrag anyways (and thought this would be a matter of minutes at most).
When I looked at it again half an hour later, I discovered it was only at 40%, and the data was now more fragmented then before, so I thought well, let it finish.
It is now several hours later (I think 5 hours), the progress is at 74% and the data is more fragmented than before - so I gotta let it run, because if I stop it now, the result is worse than in the beginning. At this rate, I'm not even sure it will be finished tomorrow morning...
I recently defragged the same drive on my netbook where I still have O&O installed, it contained the same amount of data but was much more fragmented to begin with - and it took maybe an hour until it was through. Now I don't know maybe Defraggler is much more thorough or something, but can I somehow make it not be that thorough? I mean other than using the fast defrag option, which hardly touches anything. Is there something in between?