In a properly operating system the fuel totalizer information is indeed going to be far more accurate than resistive style fuel quantity probes.
They are separate and independent functions. Whereas Fuel Quantity information is based on inputs from the wing probes to the DAU, Fuel Totalizer information is a computation within the MFD based on fuel flow over time.

Making the assumption that “both the GPH and totalizer use the same raw data, so the only possibility is a software issue in the Avidyne display” is an incorrect assumption made by many of our owners.
The piece of information used by the MFD for fuel totalizer calculations is garnished from the DAU; a bit on the data stream known as “fuel used” which appears in the fuel totalizer block.
Though it is true that “fuel used” information is a result of FF over time it is the DAU making the calculation not the MFD.

The two most common issues related to inaccurate Fuel Totalizer information being presented would be:
1. Pilot error (incorrect data entered or accepted in the initial fuel page at the time of MFD power up)
2. Faulty DAU (incorrect fuel used information provided to the MFD)
      This can be witnessed on the MFD engine page where “fuel used” will not logically match up with fuel flow.  But to check it properly, you would have to establish a constant fuel flow for a specific period of time and       see if the fuel used data makes sense. 

3.  Faulty fuel flow transducer

A properly operating system should work as follows:
• Let's say the tanks get topped off in the morning
      Pilot enters “Full Fuel” (120 gallons) on MFD “Initial Fuel” page
• Aircraft flies and let’s assume the totalizer computes 40 gallons used.
      On the next MFD power up, the MFD “Initial Fuel” page barrel should be showing 80 (120-40) gallons
      The pilot should not enter any value, but rather “accepts” the fuel shown
      This will happen on each leg of a journey, where the MFD “Initial Fuel” page indicates the last computed fuel remaining information on the previous shut down.
• Now let’s say that the aircraft is topped off again, but the pilot “accepts” the fuel shown on the initial fuel page instead of entering “Full Fuel”.
      He realizes this after he’s in flight and sees the fuel at destination is inadequate.
      At this point in time, he can go to the initial fuel page and enter “Full Fuel”
      The MFD Fuel Totalizer will recalculate fuel remaining based on this updated “initial fuel” page information along with the “fuel used” data bit from the DAU for that flight.