I agree with MP if this problem started after the fuel filter was changed, could you have introduced a small air leak? It may be so small that it would not allow fuel to drip out but as your tank level drops and the pump works harder it could draw air into the fuel system.
I once changed the filter on my Barrus and omitted to replace one of the two rubber sealing rings. It took me ages to prime the system afterwards and the engine ran rough. It was at this point I noticed the ring stuck on the bottom of the old filter and a spare one in the new filter box.