Cisco Switching/Routing :: 2960s - Swapping Connection On Both Ends To Spare Pair Of Fibers

The school I work at upgraded to Cisco Catalyst 2960-S switches, all connected to each other via fiber.  I am seeing a problem with one such connection.  Cisco Network Assistant showed a "4-Warning" regarding the fiber link port: port was disabled because it was fluctuating between up and down too rapidly.  Possible hardware problem, resolve and re-enable.  (I'm paraphasing the message...it was 'acknowledged', and I can't bring it back up.)
 
This message was only showing on our "SV-Copy-Rm" switch's port 49.  The other end, on "SV-Maint-Rm" port 49 showed a normal green link status.
 
Using Internet Explorer, I logged onto SV-Copy-Rm switch's Device Manager, and  I first tried disabling/re-enabling port 49 on SV-Copy-Rm.  It came back up blinking yellow and showing "port has bad link" when I cursor hovered over port 49.  This continued for a few minutes, followed by port 49 being disabled again.
 
The current thing I'm trying is swapping the connection on both ends to a spare pair of fibers.  I'm pretty certain I've swapped to the same pair on both ends, however, now neither switch shows an active link.  I've disabled/enabled the ports on both ends, but still no link.
 
Question: How do I re-establish the above link? (The active connection has 'fallen back' to the designated ethernet Cat 5e connection and is currently running with that connection.)