The top UNU Baron has the blue wheel box in the middle, while the bottom one has the boxes on both wheels.

I would suggest one of two solutions:
The wheel calculation is not dynamic, so what wheel is in which 'region' is determined by placement only. The other solution would be to have a manual override to hard-define which 'region' the wheel should be tied to..

This appears to happen even on vehicles that only have vertical suspension travel. My guess is that this has something to do with how my frames are set up.

I think the best solution would be to allow the option to hard-define a wheel 'slot' as part of a certain wheel group.

Fixed in V22.6.0.