Currently, it looks like most of the time is spend on defragmenting large files which are only fragmented a little bit.
How often are you running JkDefrag? My advise is only once per day. This is usually enough, even on very busy servers. Wherever possible I set programs to create logfiles per day, for example webservers and mailservers, so that JkDefrag will only have to defragment the logfile from yesterday.
It would be fine if (e.g. optionally) large files would not be defragmented if there are not "too much" fragments.
Version 4 of JkDefrag will have many options to control which files will be processed, for example an option to only defragment files that have fragments smaller than a selectable size, or have more fragments than a selectable number.