I take it this is a 4400 controller? The only reason the ports would not come up is if the link is anything less than a 1Gig link. You mention that you're plugging into a GLC-T, so it should be 1Gig capable, but ensure that the switchport is configured for gig speeds.
Also, make sure that the switchport is configured for trunking, though that shouldn't affect whether the ports come up or not.
Finally, if this is not a 4400 controller, you might need to check the opposite, and that's to make sure that the switchport isn't hard-set to a gig speed. The 2106 needs 100meg speed.