Is that all that the error message said vis "Disk Defragmenter NTFS Module has encountered a problem and has to shut down"?
Are you scanning files as well as free space?
Have a look in Event Viewer" in admin tolls and see if there is more info - follow the links to help and Support" online.
Google "defrag" and try one of the 3rd party program - here's a link:-
I know Diskkeeper gives a 15 day trial which is enough for you to sort your problems out.
I'm running XP Home, ran ckdk, tried to defrag and got error - Disk Defragmenter NTFS Module has encountered a problem and has to shut down. I run chdk and defrag once a month and my HD is 75% free. I tried in safe mode also, and same error message. I sent a report to Microsoft, any help you can give me is appreciated.