Today I went from 48.9V to 47.2V, but the min voltage says 44.9V. Might be a software issue or a spike but it occurs during every trip. I don't understand how the controller works, but is it possible that this is the issue? Does it happen to you guys as well?
The 47.2V at the end of your trip is the "no load" voltage, whereas the minimum recorded 44.9V is under full load.
Under load, the battery voltage will always drop, but some batteries will drop more than others.
You have not given much information on the batteries being used, so I'm guessing that you are using a pair of these Multistar High Capacity 6S 16000mAh Multi-Rotor Lipo Packs connected in series:
These batteries are basically intended for continuous low current use.
Although a Magic Pie at full current will only be loading these batteries to ~2C output
(32A), the voltage sag will still be very noticeable, and
dropping to 3.66V per cell under this amount of load is probably quite normal.
I use 20C continuous 30C peak 5000mAh Turnigy LiPo packs, but these also suffer from a significant voltage drop under high current conditions.
A 9C load
(45A or 45% of its continuous current rating) can easily result in a minimum voltage of ~3.5V per cell, even within the first 25% of the battery's capacity being used
(1250mAh).
I suspect that your motor is becoming "lazy" because the
controller voltage is actually reaching your minimum 44V cut off voltage under load and the current is automatically being reduced by the controller.
And I think you'll find that the 0.9V difference between the minimum recorded voltage and the minimum set voltage is caused by the additional voltage drop on the battery wires between your wattmeter, battery monitor or Cycle Analyst's shunt etc. and the controller.
Alan