With most clients, HLS chunks sound fine except for the very first fraction of a second, which sounds like it's in mono. So in VLC for example, every ten seconds you hear very obvious "audio corruption".
What surprises me is that I can't replicate this listening to the stream on QuickTime Player on Mac OS X. However, if I download a chunk and play it, even in QuickTime, I can clearly hear the moment of mono audio.
I'm using 3.6.4 build 9641. RTMP streams are pushed to a origin HLS packetizer, from which a live repeater is publishing. The packetizer and repeater are different apps on the same instance (to support failover, but that's not enabled while trying to figure out this problem).
Source => RTMP => origin (packetizer) => live (repeater) => Client
Here's a chunk to listen to: http://bethesignal.org/misc/media_147.aac