I guess I am confused here, are these phones going through the MBG or connected to a VPN or a routed connection of some kind? You say you have some kind of "short haul data link" between the two sites, is this a metro WAN link of some kind?
If there is no NAT translation between the phones and 3300, just a routed connection in private LAN space, there is no need for the MBG at all. MGB sits on the network edge to handle NAT translation to the 3300 from the public internet and is intended for phones coming in from the public internet, not phones on a routed connection back to the network.
Either way, the MBG is working properly for SIP, is likely not the cause of any audio issues in this, but you can run the MBG Teleworker testing tool (available inside the TW blade or server for download) to make sure all ports are properly translated.