3.1V is definitely too low, The throttle signal output needs to be 3.25V or above in order to produce full throttle. If you only have 3.1V going into the throttle, the output from the throttle is likely to be even lower.
This would definitely explain the decrease in speed and acceleration that you have experienced.
It will hopefully just be a faulty Hall Sensor in the throttle that is overloading the controller's +5V supply, but you won't know for sure until you actually replace it. Make sure that you get a
48V replacement throttle to match your battery, as the 24V and 36V throttles will get very hot on a 48V pack.
But, if the fault is still present with a replacement throttle, I would then say it is being caused by a weak +5V regulator, which is an integral part of the controller.
Alan