CoreAAC doesn't decode only AAC audio
Normaly he can hear the sound, so it must have allready AC3Filter installed. No need for more.
At this moment, CoreAVC is the litest filter to decode x264 streams. For a 720p you need a CPU about 1,7 Ghz but for 1080i around 2,5 Ghz. 1080p will require above 3 GHz to play. If you are under those specifications, try to disable post processing from the decoder. The file with audio problems, isn't an XviD encoded file by any chance ?