I found some time to work on this today.
First the good...
I was having some issues with my PC, which was interfering with Mach4 and causing it to lose steps. I've switched out to another system, temporarily, and I am now seeing the steps track perfectly. In fact all 3 axis show clean 1mm steps, matching the GUI jogging behaviour. So I am guessing that Mach does indeed show the commanded position, not the actual achievable position.
I am also not seeing any extra steps in STP mode. I can even use fast moves, spinning the wheel from 30 to 60 rapidly, and the axis settles to exactly 30mm from the start position. So, I think all my previous issues were the PC getting in the way.
Then the bad, for Steve ...
Neither build 4758 or 4759 work in step mode for me. This seems to be utterly repeatable. I get no motion at all. Switching to 4746 works every time.
Also, I can trigger the limit switches with with jog wheel, even with SoftLimits enabled. I would guess this is the related to the issue reported by EricSchenk, although the exact opposite symptom, since he was seeing a refusal to jog to the limit. Not the end of the world, but maybe something to look into.
Still, I have a working pendant
Now I jut need to buy a new PC:-(
Jon