I seem to remember that there are two Spanning Tree modes you can set a port into on Cisco. Fast Spanning Tree makes the port come up much faster. If that is featured on your device then it could be the issue
I was thinking of the same Huliyar and Bishop.... a STP Problem.
The Bishop is also correct, there is a command that will bring the port up immediately. Enter the config mode and go to your interface, issue the "spanning-tree portfast" command.
With the spanning-tree portfast command, the switch will enable the interface and place it into 'FORWARD' mode, bypassing the usual STP procedure.
Note, when you issue the command, the router will warn you that this command should only be used when the interface is connect to a Host, and not another other switch, because looping problems can occur.
Thanks for the feedback guys, I'll give it a shot. I didn't even think of STP. I'm too used to seeing all my other devices come up as soon as I plug the fiber in. I assume there could be an STP difference between the router module and the l2 switch fabric.