Did you do any contouring on the block? If one of your operations uses stock zero and the other uses part zero then you will have that kind of error.
bob
You mention in post #7 that you are zeroing after a tool change. If you re-zero on x and y before the counter bore then that is likely your problem since stock(0,0,0) is now gone. If you are zeroing x and y, your reference should be part (0,0,0) for that operation.
bob
Did you post this on the Fusion 360 help forums? They were really helpful in the past when I needed it.
Took another look at the photos, and... shot in the dark... but that offset looks like when I forgot to subtract half the wiggler diameter when touching off an edge. Unless you touched off on the left side of the part - then it doesn't make sense.
Or the actual stock wasn't as wide in X as you set in CAM.