Audio is encoded badly and "choppy", and channels are not respected

Recently i encoded a couple of HD videos (mkv, h264, multi-channel audio) but the audio is "choppy". English is not my native language so i don't know how to explain it well... It seems like audio is disturbed by "jumps" and a reduntant "tap-tap" in the background. It doesn't depend by the encoder since i tried vorbis, aac, mp3 and all gives me the same result.

Videos obviously play fine before encoding.

I also noticed strange behaviours regarding audio channels. If i try to encode audio in AAC format (using faac) gnome file properties tells me the audio is mono, and VLC properties tells me "ERROR". If i encode audio in Vorbis, both tell me "mono". If i encode in mp3 (with lame from default divx preset) both tell me "stereo".
But all presets are tuned to keep the original multi-channel audio! What's happening?

Oh, i have installed the latest gstreamer packages from the gstreamer-developers ppa

No files, tests, or entry points are identified in the issue. Start by reproducing the reported choppy audio and incorrect channel counts with the described MKV/H.264, multi-channel input and each encoder; done means identifying and fixing the shared cause so output audio is clear and preserves the source channels.

Written by the indexing model from the issue text.