I can't reproduce this, the Space Blaster demo works fine and plays all audio correctly even though it uses the offline cache:
http://www.scirra.com/demos/c2/spaceblaster
You should not remove anything from offline.appcache because it will break offline support (your game will always need an internet connection to play).
I think the main cause is incorrectly configured servers: if you even temporarily have the wrong MIME type set for .m4a files, the appcache might be caching the wrong MIME type, even after you fix it. Changing the URL of the game ought to fix that (after you've fixed the MIME type issue). You noted already that that doesn't work - to be able to investigate further I need a .capx and full steps to reproduce.