Fuel tanks in Orion SM always reset to Aerozine 50 and NTO upon launch no matter the type of fuel was added in the VAB

Sounds like you're using RealFuels (and maybe RO?) ... in either case the configuration for that is maintained elsewhere.

Okay so it isn't an issue with SSTU?

I don't think so. Highly pressurized tanks are a RealFuels thing.

Edit: Actual, not confirmed. The fuel selection appears to work fine in my testing; select MonoPropellant in the VAB, and that is what is in the craft upon launch.

Any specific configuration needed to trigger this issue?

Well when I tried to use Orion SM it said the engine had flameout because of lack of pressure, then I checked and realized the AJ10-190 engine ran on MMH and MON3, so I added those tanks, along with the preexisting A50 and NTO tanks and it just went back to A50 and NTO. When I switched RCS to MP, it removed all non MP tanks instead.
It seems only fuel tanks which the rcs is set to use stay in the vehicle.