QoS Over PepVPN

We have two offices that use our cloud-based VOIP service and they are connected via PepVPN. Their phones work fine until a person at one office calls someone at the other office.
If they place a site-to-site phone call, the audio is extremely poor. Is QoS not being maintained over the PepVPN, or is something else going on? Both routers are Balance Ones on the latest 7.0 firmware, but this also happened with the 6.3.3 firmware.