You will need to check your interface configuration for the second set of switch ports. When you create a virtual chassis the interface numbering increases the FPC number on the interface for the new switch from 0 to 1 so instead of ge-0/0/0 you have ge-1/0/0.
I suspect that with this change there is no configuration on your new ports you you need to add the port level configuration you need for the site on the appropriate interface numbers.