So, I was reading this post: No audio in Mpeg streamclip - MacRumors Forums
So I'm essentially having the same problem with an .AVI to ProRes 422 .MOV conversion... no audio (in any format). HandBrake converts them to mp4's just fine with AAC preset.

Someone on that thread on MacRumors said that downloading the old version is the answer to this, however the link they gave doesn't work anymore. Does anyone have either a 1.9.1 they could wrap up and put on a download link or a working link that already exists?

I have Perian, Flip4Mac, and all the Final Cut X pro Codecs (Just bought it). I have also followed suggestions about Audio PID drop-down menus to no avail.

I have no other option at this point because the only thing that converts with audio is HandBrake! (in cruddy 480p mp4 files, then back to ProRes with MPEG Streamclip)