I've used Defraggler 2.09 for days on end on production database servers (Windows Server 2003/8 R2 on Dell 2950, R710, R910, etc.), without any known issues.
Recently, I tried 2.10 on a Hyper-V host server (Windows Server 2008 R2, Dell R510, the C: drive), and was unable to start a Hyper-V guest because it was unable to access their equivalent of a REDO file (odd, since I thought the guest had been shut down, not suspended). As soon as I stopped Defraggler, the guest was able to start.
Unfortunately, that's a production box, so I'm generally unable to repeat any tests, but I did want to report the time correlation of these events.