Two chargers on the same battery will have slightly different charger voltages. So the "spread" between the charger and battery is greater with one than the other. When the battery voltage rises to be the same as the lower charger voltage, no more current from that one while the other brings the battery voltage up to its so there is no more spread there either.
When the battery voltage is lower (more load or less of a state of charge) so there is spread between both, the current from the smaller spread will be less than from the larger spread in proportion to the size of the spreads. Only if the two spreads were exactly equal will both currents be the same amps.
Even if the two controllers were identical in voltage their wirings to the battery will have slightly different voltage drops.
But that's not all.
Output current with MPPT controllers (have a buck converter) come from the watts at each controller's output, divided by battery voltage. Output watts is input watts less controller efficiency. Input watts is array watts less line loss between array and controller. Even if the arrays were the same, the watts would be a little different. But as you noted, you have two different wattage arrays, so you will have different output watts and so different output currents.
However that still leaves the situation where charger current can be different but with identical voltage spreads, one would not drop out first.
The mystery would be why is it not always the same controller that "drops out" first? Perhaps at times the 400w array is shaded or at a different sun angle (slight opposite roof tilt each side of the RV?) so it has fewer watts than the 300w array?
At very low battery acceptance rate (battery near full or full and overcharging) the thing could tip either way where at times the 400w array has less output than the 300 but also has the higher voltage drop to the battery?