Unfortunately MP graph building is not wise enough to handle such situations. It loads only the filters and lets directshow to do the rest. In your case ffdshow has bigger filter merit valua and directshow will use that instead of the AC3Filter.- In MP Configuration, under Videos -> Video Player: set AC3Filter as the "MPEG / AC3 audio decoder". Set ffdshow audio decoder as the "AAC audio decoder".
MPII will handle graph building in different way (most likely).