Cisco VSS, Domain ID and Virtual MAC Addresses

The other weekend I connected a L2 circuit between two sites. At both ends were Cisco 6500 Catalyst switches running VSS. The interfaces they connected to were configured as L3 and EIGRP was run between the two sites to share routes. But as soon as they were connected the neighbors started flapping. Troubleshooting started and as always you start at the lowest OSI layer and work up. Bingo! The issue