Very timely post. I just found out this week that there are known issues with some of these radios. Lots of them are functioning perfectly but I don't know the rate of failure. I've been chasing similar problems with my Dynon Com for nearly 4 years now. I did similar troubleshooting as you, triple checked the wiring, swapped com1/com2 audio/PTT wires from the audio panel between Garmin and Dynon radios, swapped antennas and cables, the problem always stayed with the Dynon radio and the other was still OK. They replaced the first radio within a week of first flight back in Oct 2016 for the same complaints I still have. The radio replaced again last summer with their newest version, thanks to Rob Hickman at AFS when I stopped in for a visit during a vacation trip. I thought it was finally fixed but I still get complaints from ATC and other pilots on audio quality sometimes. Often the first 3 or 4 seconds of a transmission the carrier is present but there is no modulation. I had an avionics tech check the installation and everything was verified correct according to the installation manual. I have a digital in-line radio test set that measures transmit parameters (Tx power, modulation, VSWR, etc) and it shows the delay in modulation. Rx is always very clear.
Give Dynon support a call. They are great to work with. They are shipping a Trig radio to me at a cost of $450 and I have to return my current one. I assume it is a discounted price and I have to pay their cost or something since it is no longer under warranty, unfortunately. I'm not thrilled about the cost since it never worked properly but it will be an acceptable cost if I can finally be rid of this nagging problem. It should arrive soon.
Colin