After a little reading I think I figured it out. I replalced the HD in the laptop and wanted to make sure everything was OK before I proceded without exceding my learning curve.
From the info at http://www.viztaview.com/tips/37-tips/57-sysinternals.html I ran NTFSinfo on http://live.sysinternals.com/ site and it says I have a MFT zone size of 2094MB. All the math comes out right with JkDefrag excluding the MFT zone in the free space calculation and the Win GUI including it.
Sometimes old is gold.