Have you considered evaporation as a very likely cause of the reduction in MPG when you empty the entire tank? I beleive this is the most likely cause.
First of all, everyone who is mentioning the inaccuracy of the gauge is missing a critical point. It doesn't matter. What we care about here is the miles:gallons ratio. That is all that matters. You are using the same odometer & pumps that are likely VERY accurate...regardless, the error will average out since you have the same error in every mile & every fill up. For this purpose, we can assume that the fuel gauge & pump are perfect.
Now, on evaporation...consider the environment your gas is in. Keep in mind that gasoline:
Fuel injected vehicles have a "loop" type fuel system...basically fuel is constantly flowing to the engine, through the fuel pressure regulator, & back to the tank. A VERY small amount flows through the injectors. So basically you are constantly pumping gas up to the engine, then draining it back in the tank. The problem is this heats the gas up significantly.
Also, as you probably know, gasoline evaporates, quickly, much more quickly than water. Its boiling point is about 150*F-160*F. Pour 1oz of gasoline on a peice of black tin in direct sunlight...also pour 1oz of water on the same peice of tin. The gasoline evaporates MUCH faster.
Also, think about how the inside of your fuel tank is practically constantly coated with gasoline due to the sloshing from stopping, starting, turning, bumps, & just vibration. This means the surface area of gasoline exposed to air is always kept at a maximum. The more gasoline you have in contact with air, the faster it will evaporate. Also keep in mind that at 1/4 gallon, there is 3x as much air in your tank which will have evaporated gasoline in it. Anytime this air escapes your tank, some gasoline escapes with it.
In fact, gasoline evaporation is such a large factor, the EPA is starting to try to control it. That is why a loose or missing gas cap on an OBDII equipped vehicle will throw an SES light. The gas cap must be able to hold a minimum amount of pressure in the tank...if it is loose or leaking, a large amount of vapors are allowed to escape.
It would be very interesting if someone used a more scientific approach to determine the effects on mileage that filling up when empty vs. filling up when 3/4 full will have. Just alternate by months...on odd months, fill up when your tank is 70%-80% full. On even months, fill up when the tank is near empty. Remember the gauge doesn't matter, just keep an accurate record of miles:gallon, by taking the readings from the pump & odometer. I think you would see a measurable increase in mileage, & I think that probably 80% of your increase in mileage would be due to a decrease in gasoline evaporation.
Thoughts?