GRT Avionics

has anyone else checked the fuel quantity before engine start and after?
I see a 2 gallon reduction in fuel quantity with the engine running for both tanks.
it seems to be voltage related, if I shut the alternator off the system voltage reduces and the fuel quantity goes back up.
the resistive gauges are wired to the HXr analog inputs using the internal pull up resistor.
Any ideas?

It's probably the internal pull-up voltage that's changing with the power input voltage. If the input voltage is too close to the regulated voltage that supplies the pull-ups, then the regulated voltage won't reach its target voltage. The high resistance of the internal pull-ups compared to the probe also makes the inputs sensitive to voltage changes.

Ok thats what I was thinking, how do I calibrate the sensors without running the engine?

You could put it on a battery charger on float mode. Should raise buss voltage up to 13.5 volts or so.
Better way: Are you using an EIS? If yes, run the fuel floats thru it per the manual, using 470 ohm bias resistors to the EIS 4.7 volt regulated supply.