Hi Christopher,
In my understanding this statement:
"As expected elrp shut down those two ports and the backbone ports(ex 1:53 ) on both switches."
Is not expected.
It should shut down one port. If you don't have the uplinks in the exclude list, they might be the one shut down. Actually, by default, the port being shut down is the receiving port where the ELRP PDU is received. This can be change by configuration starting with 16.1, as Bill stated.