Try opening a command prompt (go to Run, type cmd) and cd to the folder of shn's in question. Then do your shntool commands on them instead of using the contextual menus from Explorer. That may work.
Also Terry, I've noticed the same thing with the most recent version of shntool. If you're unable to repair the last track SBE you could open it up in CD Wave and cut off the last frame, or bring it into WaveLab or SF or whatever and trim off the last frame. A little more work but it doesn't require you choosing more than one file to shntool fix on.
Hope this helps.