Sounds like you have a routing issue in your VPN network. Basically, if you have your IP phones on voice subnet, you will need to route this through the VPN for all phones to call back and forth. Remember, CallManager or CME will setup the call between (2) IP phones, then after the calls are connected, it drops out leaving only IPphone---to---IPphone. Is the two subnets can not be routed between the two phones, you will have a phone ring, then probably have no audio.
good luck!