Check your CSS on your Voice Gateway routers. I had a similar problem when trunking between our Meridian One and our CallManagers. Set a CSS that has all of the partitions that you need the Voice Gateway to be able to reach, then apply it to the gateway. If you are using MGCP, you will have to reset or restart the gateway (which sometime doesnt work, at least on a VG200). Sometimes I need to phsyically restart the router or issue a clear MGCP to accept the new settings. I am not sure if this is your problem, but I hope it helps.
Matt