Anyway to reset the ports with the IOS? How can I troubleshoot to make sure they are bad and not just something with the IOS.

this is what I get from a reload

00:00:09: %LINK-4-ERROR: is experiencing errorsFOUND an unknown transceiver on

port 5

FOUND an unknown transceiver on port 6

FOUND an unknown transceiver on port 7

FOUND an unknown transceiver on port 9

FOUND an unknown transceiver on port 10

FOUND an unknown transceiver on port 11

FOUND an unknown transceiver on port 12

port 1, 5, 6, 7, 8, 9, 10, 11, 12 are orange and the SYSTEM led on the front panel is also orange.