Dave, That is the limitations of stall homing. I am sure you have seen that when the axis hit the stops when homing they jump back after they hit. The home is set to 0 after that jump back occurs. That jump back is one thing that is not consistent. Another thing is junk buildup between the axis blocks and the stop blocks. This is what I have observed, I am sure other will clarify if I am wrong on some points.
Here is one thread that discusses using limit switches to overcome these limitations.
Can you add limit switches
I have not done this because 1. it adds complexity to the machine thus more things to fail 2. there are cheaper ways to get accuracy, however they take more time.
I won’t have time till the weekend to take pictures of my setup. But if you’re using fixtures already then you are well on the way. If you are taking your piece off for pours or whatever maybe you can rebump the fixture to get origin before you put the piece back on.