Happened again last night. Clocks are at stock now.
I'm still not sure whether this 'disconnection' is something to do with the miner or the card. Is the driver crashing? Do you have another program that will stress the card which you can try running after a 'disconnection' to verify that the card is perfectly happy? Could you try different mining software for the second card?
Are you pool mining? If so, are you sure that you are not just disconnecting from the server? Perhaps try a different server or, better yet, solo mining, and see if the 'connection' problems persist.