It sounds like you are using After Effects as an editor. It's not really designed to do that. You use AE to create shots or short sequences and you edit in a NLE like Premiere Pro. The sound tools in After Effects are also very limited.
Your frame size is also very odd and depending on the compression format may be giving you some of the problems you are having. If you purged all memory and cache before rendering a RAM preview and then purged everything again before rendering and you rendered to a codec that supports your frame size (h.264 MP4 does not) then it's very hard to say exactly what is going on.
If this were my project I would have started the project in Premiere Pro and only used After Effects when I needed to do Effects or Composites that could not have been done in AE. If you have about 100 layers and most of the time 4 of them are visible at one time and your video is fifteen minutes long then the average comp would be about 36 seconds long. That's still a long time for an AE comp.
If you want to keep all of the work you have done in After Effects my suggestion would be to try rendering out a separate audio file and make sure that works fine. If everything else in your render is OK and you have rendered to a production format and not to a highly compressed delivery format (MPEG) then you can then create a new project in Premiere Pro or AE and add your rendered movie and your new audio track to the new project, turn off the audio in the movie and use the audio that you fixed. If you rendered to a compressed format then you could select your original comp in the Project Panel, create a new composition from the original comp, turn off the audio in the timeline and then add in your repaired audio file.
If you cannot get a good audio track I would set the work area to the portion of the project where the audio works and render audio just from the parts that work and then mix the tracks in Audition to get your final audio.
Thank you for this very detailed answer!
I chose AE for editing, because Premiere Pro was not able to do the "transitions" that I was looking for. (a camera moving from one interview to the next).
And I chose the format, since the footage is shot in miniDV, which is very blurry, when you show it even on a little screen, what I intend to do.
To export even a little part of the film as an audio file (aiff, wav) does not work properly either. The programme seems to have problems with the fades even with a short part of the film.
What do you mean by your last sentence : "...mix the tracks in Audition ..."
Can I export parts of the composition to Audition, edit the sound there and reimport this edited sound into AE? (like with Premiere)
You can animate position and scale in Premiere Pro. You can even distort so that it looks like 3D.
You can export an entire track into audition by rendering just the audio and opening that in audition. You can Edit an individual video or audio source in Audition by selecting the layer in the timeline or the resource in the Project Panel and using Edit>Edit in Audition. You cannot generate an audio track from a composition and edit that in Audition directly. You have to export the audio using the Render Cue or the Adobe Media Encoder.
I don't know everything about your project but in most cases there's a much better workflow to try and edit a 15 minute video than doing it all in AE.
I am very busy this week and will answer next week!
Maybe have to upload a little part of the film to demonstrate more clearly.
Thank you for your thoughts!
There I am again! Sorry for that long pause!
In my film I have a camera moving from one interview to the next, pretending to have 8 interviews simultaneously on the screen. So there are times, when you see 5 videoclips during one camera movement. Is it really possible to build that kind of movement in Premiere?
Now I took your advice and rebuild the audio in Premiere using the Image I got out of AE. And it is not too much work!
So thanks a lot for your help!