My apologies are due to you Jon, because I cannot start my analysis from an irrational position. If there was “NOTHING different” between all of the attempts that were both successful and unsuccessful, the results should not have varied by the slightest amount. Any significant variation from your desired datum demonstrates that CNC machining is a useless pursuit. Where you cannot rely on the final result, the implication is that something in the continuous chain of factors which MUST BE PRESENT for successful CNC machining… was not present.
Logically speaking, you will only discover that crucial factor by painstakingly removing one of the factors in your system and looking at the results obtained. Replace that factor and remove another one, then you can examine the results… ad nauseam. Something MUST be a causative factor and from this distance, I could not begin to guess at what that cause is. If you generated some log data, that would really help to pin down the cause.
Mechanical things do not usually give random results unless there is a fault in the driven elements, or one of the driven elements is poorly attached. Electrical things do not usually fail intermittently and cause interrupted results. They either fail and are non-functional or they work. Software can and does fail intermittently. It may have been tested insufficiently. A specific variable has not been considered and accounted for. This leads to unpredictable behaviour and unwanted results. It may even be very poorly written. Software can also be used in an unintended manner (by the user}. You may have to search the Carbide 3D forum archives to find a similar failure to the ones you have described and illustrated.