If I write extended debug information a see a lot of malloc() errors.
Esprit is right, JkDefrag is simply running out of memory to store information about all the files on disk. I have it on my wishlist to test for this eventuality and gracefully stop with a nice error message, but the current version will continue and try to process the files about which it has information. There is no commandline option or anything like that to lower the memory consumption. I am hoping version 4 will use less memory, on which I am working right now.