I suspect the difference in fuel level refered to in the flight operations manual is for an an inflight situation where the leaking cap gasket allows a slight vacume to be drawn on one tank.
I assume that you are not just talking fuel gage readings. On the ground (and in the air) my gages never read the same, but it is the gages, not the amount of fuel in the tank. I have confirmed this with actual fueling tests.
Also, I assume you have alternated which tank you fill first. I have noticed that when I fill the tanks, the first one that I fill will always take a slight bit more fuel than the second. This is because fuel is draining from the first to the second until I get around to getting the second tank filled. I never have noted the exact amount of difference (and it would be time dependent), but I have the impression it's about a half gallon with my usual procedure.
Hope this helps.