This is a hard one to nail down. Looking at Topology view for one of our switches:
"Cisco NX-OS(tm) n5000, Software (n5000-uk9), Version 5.0(3)N2(1), RELEASE SOFTWARE Copyright (c) 2002-2011 by Cisco Systems, Inc. Device Manager Version 5.2(1), Compiled 6/13/2011 6:00:00"
shows connectivity to 6 other switches. Problem is that it isn't connected to any of those switches. All Switches also seem to be connecting to Ethernet 1/2 of the above switch(found by dragging over the links in Topology Map).
I'm not sure where to start here as we do have several discovery methods enabled. Potentially I could nail this down to a code path with some procedures on resetting the link discovery data.