Not much is revealed here. You should have battery logging and configure the Dynamic Notch filter. Start by setting INS_LOG_BAT_MASK to 1 and make another short hover flight.
Battery voltage is the most important so you can use the thrust linearization features. A simple voltage divider is better than nothing. The Cube Orange has a 3.3V full scale input for battery monitoring.
Ok i will have to look into that because we are running the pixhawk off a separate lipo. Gonna have to do some research into the 3.3v input you refered to.