figured out what the problem was. The laptop I was using to program the Cisco switches had been used the previous week to program some PLCs, so the laptop ethenet port was set to 10MBs/Half Duplex. The running-config of the switches has "speed 100, duplex full" set for all the ports. So before the configuration was loaded, the ethernet port connections worked, I didn't notice I was connecting at 10/Half. Once the Restore was done, it would drop all connections like the laptop trying to connect at 10MBs. So all the ports 'appeared' to be dead, when they were just waiting for a 100MBs connection.