Ok, the machine seems to be performing mostly correctly now. I'm still seeing my macro probing the wrong direction occasionally, but I haven't caught it doing that in the last half-our. So I'm going to mark this as "solved" since my problem of the head occasionally not lifting seems to be fixed by the updated firmware.
If I can find a clear pattern for when the probing macro probes "towards the workpiece" in the wrong direction I'll open another question.
Thanks again for the great support!