This is what I could find from the Diskeeper website concerning your problem:
"I have installed Diskeeper but it will not defragment my system or it does not complete the defragmentation.
We have not received any verifiable reports of hangs or lock-ups with Diskeeper on FAT or FAT32. What we have seen is Diskeeper taking a long time at specific points in its operation. We advise that you use Set It and Forget It to schedule Diskeeper to run in the background.
If you would like the run Diskeeper manually, you should find success in allowing the software to complete its operation, which may take time.
If the drive does not have to be accessed by an operating system other than Windows NT, 2000 or XP, we would advise you to convert it to NTFS.
Our developers are working on faster FAT32 engines."
For Diskeeper support click here. To contact Diskeeper support - [email protected]. Good luck, G