Max bus voltage is a scaling factor, it is not the nominal voltage of the system, but rather the maximal measurable voltage by the hardware. It is used to scale the small voltage going into the ADC to the real voltage in the bus. The ADC maximum voltage range is 3.3 volts, so any measurements have to assume that the maximum voltage in the ADC is the max voltage of the system, which, if you make the numbers, for a 49.9k resistor, that works out to 54.89 volts.
48 volts showing 2.7 volts in the ADC input is perfectly reasonable and since there is a scaling factor to 55 volts, then you can calculate:
(2.7/3.3) * 55 = 45 V. Which is within range. Now if your input is actually 48, then there is potentially a problem either with your max DC bus (like I said, the number really works to 54.89) and the tolerance of the resistances used.
So regarding overvoltage, remember Maximum DC bus is simply the scaling factor, it does not mean anything except tell the ADC its measurement range. Once that is set, then all your voltage readings will work out. The over voltage is triggered by the Over-voltage value field in the protections block.
By the way, with your original value of 40.2k ohms in the resistor divider, a 48 volt input would actually mean 3.5 volts at the ADC pin, which would mean more than any max DC bus, because the DC bus is scaled to 3.3 volts, so of course you would always get an over-voltage in that case, plus all the other strange errors you were getting. Better go with the 49.9k.