Ok – sorry to re-hash an old thread but this may come in handy for a lot of people as it seems to be a common complaint 🙂
I ran into this problem today – I had a pre-comp which was playing audio correctly and then in the master comp the audio was muted. The layer audio was definitely turned on and no keyframes applied. WT…?
The clue was the audio would play if I solo’d the layer. So I started turning other layers off until I found the culprit!
Because I was using the same pre-comp in a number of different cuts in the main timeline it turns out the if ANY instance of that pre-comp has a time re-map effect on it and appears in the comp and that time re-map effect includes a freeze (mine did – I haven’t tested but i suspect any time-remap will have the same effect) then all the audio for any layer with that pre-comp gets muted. The solution is simple – turn of thaudio for the layer with the time re-map effect on it (after all it appears you can’t use time-remapped audio in AE anyway:)
I’m not sure if this is documented anywhere but i couldn’t see it in the help file – really audio should only be muted for the time remapped layer (so it is a bit of a bug) but there you go – problem solved!