I am confused by this behavior. Using bitzero and bitsetter to probe a square aluminum bar. Once everything is set up I clear all offsets and probe corner, start the job, and after measuring the tool with bitsetter the program runs 2 mm ABOVE. I then stop the running job and probe the corner again and start the program as before and now I’m on target. Why is this? This caused a broken endmill after I tried to correct the offset and when the tool changed I didn’t realize it was 2mm BELOW now because the next tool probed correctly.
Being 2mm above material is similar to what would happen if you used the bitzero to probe XYZ but happened to lay it on top of the material rather than sitting on the corner, overhanging. Any chance this could have been that ?
Else, did you happen at any time to change the tool without being prompted by CM to do so or without using the change tool button in CM ? That can throw off the Z offset too
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The bitzero was on the corner and not on the top and yes I made the offset without being prompted by CM but it made sense and would’ve worked if not for this probing error. I’m gonna try to put it into a routine for now. Probe, home, probe, start job. Ill see if that makes it consistent at least.
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That is the proper order. If you don’t set the height at all times you replace the bit, then the machine doesn’t know the length changed. 
I refer a lot of people to this C3D blog post:
In essence NEVER replace the endmill / bit / pin without doing a “load new tool”.
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This doesn’t sound right. That means you are clearing the initial tool length offset that should occur right after initializing, or as part of initialization. Try the whole process again without clearing all offsets.
Initialize, let it probe whatever is in the spindle
set your zeroes with the same tool (or probe)
Then run your file & let it probe the tool for the toolpath (even if it’s the same tool).
If it is the same tool, look at the current Z value before you hit OK to let it measure the tool.
When it retracts after measuring the tool it should be the same.
If a different tool, you could measure the previous tool, change tools, measure the new tool & get an idea of what Z should be after it measures. If it’s not close, stop & recheck your zero before proceeding.
I’ve gotten used to watching Z before & after toolchanges as a sanity check.
Interesting read. I also had a incident with 2mm too low ( I wrote it up a while back ), it was only once in a row though and I could not repeat it. 
it was very a simple work flow, I zeroed off the waste board with the BitZero V2 so there was no oops on a corner or an edge. First cut was a surfacing cut and it hit too deep. I stopped the job. Manually check zero and I was 2 mm low ??? Did the same thing all over and it was fine this time. I just assumed it was a glitch
However I now have trust issues with the BitZero I now always double check the zero manually and prefer to set it manually. I just find it more accurate for now and I can see it directly for myself
I am sure me an the BitZero will get to a good place, it will just take some time
When I want to just zero the Z and not use a corner. I flip my BitZero upside down on the stock.
Just make sure the Bit lands on the aluminum and not on the plastic.
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