JkDefrag -a 2 "C:\"
The problem is not caused by JkDefrag, but by the odd double function of the backslash. Windows uses a backslash not only to separate subdirectories, but also to escape special characters. Look at the logfile and you will see that JkDefrag receives 'C:\"' in your problem case. Notice the double quote in there! Perhaps it will work for you if you specify "%P*" in the mask (notice the asterisk), instead of "%P".