Call signaling is working because it is between the Callmanager and IP Phone, not the two phones. Have you tried pinging from one communicator to the other, I bet you can't do it. The problem here is that a typical VPN configuration does not allow two remote connections to talk to each other. It sounds like what you need is Dynamic Multipoint VPN or DMVPN.

http://www.cisco.com/en/US/partner/products/ps6658/products_ios_protocol_option_home.html

DMVPN allows two remote locations to have a direct IPSec link between the two of them to pass traffic directly without going through a hub location.

Another thing to check is to make sure that your audio traffic is being sourced from your VPN interface. You can verify this by going to the preferences menu, select the "Audio" tab, click the "Network" button and verify that the "Audio IP Address" is that of your VPN interface or the interface itself.

If you can't implement DMVPN and you find that is your problem, you can always hairpin the audio through a gateway as a temporary solution. If the communicators have DID's, just dial those instead of the on-net extensions. Obviously that will tie up two channels of your PSTN dialtone, but it will temporarily solve the problem.

Let me know if that is helpful.