I searched the forum with no big success. Many people seem to have the no-audio problem with multicam. My problem is different.
I enabled the multi-cam feature in CS4.1 in the preview (source) monitor. I have 2 video tracks (1 MPG, 1 AVCHD). Both appear and are in sync. Also the audio is in sync as long as the multi-cam feature is turned off. As I turn it on and play the monitor, it's totally out of sync with the video. Totally means, that it's really about 40 minutes away.
My only recommendation is to just not use GOP-based media. It's a bad idea at it's core and issues like this are not uncommon.