Strange behaviour there from Diskeeper. What happens when you use Windows own defragmenter? What's your OS & Diskeeper version, please? Have you tried an uninstall/reinstall? If you have a paid-for version you may be entitled to free support click here.
I've been having problems with Diskeeper as well (the Lite free version on Win98se). Problems began ever since I installed a second hard drive some months ago. I have a total of 7 (3+4) partitions on the drives. Invariably I need to use Windows own defragmenter (after shutting down background programs) to get the desired level of defragmentation. Tried a uninstall/reinstall with no change. G