Right now my money would be on Van's #1: two queens, one either side of the QX.
So - you could try splitting the boxes, placing them reasonably close together so that the foragers will enter both, and any re-combining will be easier. If one of the colonies thus created becomes distressed, that suggests queenlessness within that box.
Otherwise - wait 3 or 4 days, then look for eggs in both colonies. If you have eggs in both, then you know well-enough what the situation is. If you don't - then the eggs will indicate the queen's location (obviously).
Whilst those boxes are split apart - check that QX very carefully - if it's wire, look out for the slightest distortion which could allow a queen to squeeze through it. Sometimes wires become bent upwards or downwards, so that their spacings look ok from above - but if you look at the wires from an angle, you can then more easily see larger gaps which such distortion creates.
LJ