OK, think I've got it.
If you select the loop length on the transport by typing it in, it snaps to the bar and displays correctly on the transport, which is what i did at the start of the GIF.
If you then select the loop length by dragging the cursor in the timeline, it snaps to the sample and displays the wonky value on the transport. It is snapping to the sample after the bar at bar 3 and at bar 4 it is snapping to the sample before the bar which is causing the rounding issue you get on the transport.
Guessing simply doing "Loop end value" minus "Loop start value" = "Loop length" would break some other stuff???