This one was interesting to get to the bottom of. @JaredBusch With the VPN tunnel enabled, the phone system was trying to send RTP to the phone on the internal IP. There is a setting in FreePBX on the extension level called "RTP Symmetric". Normally, this is set to yes. I changed it to no and the audio started flowing normally. However, I didn't like this solution. So, as a test, (and what I should have done from the beginning) I blocked all outbound traffic FROM my phone system, to any local network. (10.x, 172.16, 192.168, etc) This immediately solved the issue. I did not yet do a packet capture AFTER the fact to confirm, but I am assuming that blocking the PBX's ability to get to an internal private IP, forces the system to renegotiate and send the RTP to the correct public IP.
Definitely an odd issue.