When I ran,
start /b /low JkDefragCmd.exe -s 1 -a 3 <filename>
JkDefragCmd.exe stayed on without terminating, though the size of the file to be defragged was less than 1MB.
Having left JkDefragCmd.exe that way for 24 hours, I found it was still there.
I manually terminated JkDefragCmd.exe and then ran it again, with "-s 5", and it took less than 5 minutes to defrag the same file.
I have seen similar situation a couple of times since. However, I haven't been able to intentionally make it reccur.