Did you ever figure this out?
I had the same issue. But it may not be the exact same cause.
I turned on 'g729 debug' in the asterisk cli with verbosity at 10 and saw in my case it was getting a ton of 0 length packets.. Which I certainly found odd. I believe each zero-length packet would trigger the packet loss correction routine build into the g729 codec in Asterisk 13. But it did NOT trigger it in asterisk 1.4 and I confirmed the machines on asterisk 1.4 where seeing the same 0 length packets but not doing anything.
It turned out to be settings in my Cisco gateway I am using. In my Cisco Gateway, I had comfort noise disabled but not VAD. This meant that zero-length 'comfort noise' packets where being sent. I am guessing they triggered false PLC execution which then mangles the otherwise perfectly good audio stream.
I did some research reconfigured a few things and verified vad was turned off in the cisco gateway and magically the errors went away and the audio is crystal clear.
So basically you want to make sure comfort noise and Voice Activity Detection type stuff on anything connecting to asterisk 13 with g729.
Hope this helps someone. Cause it was a nightmare to find/fix.