Datum alignments can produce surprising results from time to time because a datum could be flipped. This can happen in a couple of scenarios:
A simple point measurement uses the line of sight from the instrument to the point to determine the positive side of the part. If you measure using an 1.5” reflector it is easy to measure around a corner, but in that case you need to identify that within SA.
Open slots or mid planes have a direction that also needs to be controlled.
Finally you can measure a part indirectly such as measuring the table top to define the bottom of the part.
Datum alignment control is handled within the Datum properties.