I'm having trouble exporting a Quicktime from ASP and retaining the 48khz. I can't find the Project Audio settings either?
I've animated to a WAV at 48khz but when I export it it seems to turn the file to 44khz. Then if I replace it with the original WAV it's all out of sinc.
On the Mac the Quicktime panel doesn't give me any audio options while exporting from AS. Any audio should be included "as is", and I never had any trouble with it. (I get audio and other options when I export from Final Cut.)
You should check your general audio and quicktime settings.