I am experiencing this same issue with version 3.7.  It seems that JkDefrag is attempting to expand the gap by moving a few clusters of data out a couple of clusters at a time, then checking to see if the gap is large enough for the file... this continues until the gap is large enough.  

May I suggest that if the file you are attempting to squeeze into the gap is larger than the block you are moving, that you move the block to the beginning of the gap instead of pushing it out a couple of clusters?