I'd have to get mine all hooked up to tell but it's all put away right now. Off hand I'd say that his patches could be stored with the short board and it's confused with the long board connected. Try saving and reloading some patches with the long board to see.

Other than that maybe you should try a new CAT5 cable, they're cheap and avaliable enough and it's uber easy to do. Just don't do something silly and use a crossover cable. Using a crossover cable is likely to do some bad things. 

If none of that then it's probably something simple like a loose connector inside the FBV or maybe a bad pin in the CAT5 cable connector but I don't think so, that would likely make the whole board inop as it's serial data being swapped between the Vetta and Foot controller. Since neither the switchs or the LEDs work, that's somewhat telling.