The audio is probably on the wrong tracks because your recording settings were set to channel 3&4, not 1&2. AE still only does stereo and simply doesn't see extra tracks. no chance. you need to extract the audio in an external program and import it as a separate file. Premiere should be able to handle this, but feel free to use otehr tools.
Hmm the audio used to work during AE 5.5. What do you mean its on the wrong track? Thanks