Fuel measurement is ultrasonic with something in the region of 20 probes per tank (depending on a/c model number) with ultrasonic densitometers also bought into the equation. As previously posted there is some 'leeway' in the difference between actuals and uplift calcs. Also there will be a certain amount of aeration of the fuel after uplift and the true indication can sometimes take a while to settle down.
Failing that it could be water....