I'm using the developer version with Wirecast.
To record the live stream I'm using the "record-live" StreamType and use the mp4: prefix.

The audio in the recorded mp4s gets completely out of sync.
I didn't try it yet without the mp4: prefix but I've recorded the raw live stream with rtmpdump and it doesn't have any issues as suspected.

This is the media info of the server side recording:
http://pastebin.com/DSL2sTvK

This is the media info of the raw recording:
http://pastebin.com/TdtA0qi9

My guess is that Wowza doesn't regard the variable frame rate when muxing the streams into the mp4 container.

I'm not sure if the sync issues also happen with the default server side recording. Gonna have to try it out.

Regards