LMS, specifically the ANI Discovery Process of Campus Manager component, relies on Cisco Discovery Protocol (CDP) to ascertain devices and their connectivity. Since CDP is a Layer 2 protocol and GRE is, in effect, a Layer 3 virualization; you will likely see the devices at the "other end" of the tunnel as unconnected to your main campus or network core. I don't believe there's a work around for this. You will need to seed every remote (across a tunnel) site with at least one device to discover it properly. Also, don't forget to synchronize RME from Campus manager to keep your inventory up to date.
