I have had the same problem, but with a much smaller drive - a 160 Gb SATA drive on a laptop (MPC TransPort T2500 stuffed with 4 Gb RAM.) My error message reads:
MyDefrag.exe - Fatal Application Exit
Oeps! Memory full while running MyDefrag in function 'TreeNewNode' in source '.\Tree.cpp' on line 70.
It always happens in zone 4 of 5, somewhere around 85% complete. Oh, and the drive is pretty full: 149 Gb is occupied.
Follow the link Jeroen has posted and post a logfile.