Ignore this, it turns out the grub screw had fallen out of stepper motor, there was slippage but oddly it seemed to create the above effect... which frankly I think I'm imagining since I can't see why it would do that.
Good outcome!
It may have been confusing with movement due to vibration, or the grub screw could have been binding occasionally.
I read your post earlier and could not think of anything to add as you had a good check list of things.
I have just had these exact symptoms. I had disturb the wiring whilst I was replacing a part. When I switched back on the Y axis seemed to be reversed. On further investigation I found that the y axis was homeing in the wrong direction and eventually hitting the - y stop. But it was ok if I moved the bed in either direction using pronterface. On investigation I found one of the wires detached from the homing switch. Replaced it and all was well. I wonder if in gregstah case he had the same problem and in tighten the grub screw fortuitously remade his home switch connection. It may be worth re checking the switch connections.
Omerod 096