Is this a new virtual chassis stack that you are just starting to use ports on the second switch?
When you join a new switch to the stack all the port number change the fpc position, the first of the three numbers goes from 0 to 1. I've seen where this affects all the ports to no longer have any configuration at all and are essentially then dead for connectivity.
Confirm the port numbers for your switch using show interfaces terse
Then use show configuration interfaces and confirm there is the expected vlan setup on the affected ports.