I had the fuel tank cleaned and the carb rebuilt on my '49 Super earlier this year, and my fuel filter doesn't fill completely either. I'm running an electric fuel pump, but the filter is always 1/2 full or less when idling. The car runs and performs fine, so I don't worry about it. I was talking with a guy that owns a '52 Roadmaster at a local car show recently, and we were discussing this...his car does the exact same thing. Before I had the work done on my Super, it was starving for fuel, and the filter would have no gas in it. Turned out that the needle valve and seat were the culprit on my Stromberg carb, maybe that is something you would want to check into.
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