I think that the non working switch is part of the problem. It may not work because it does not get signals from the limit switches somehow. A bad switchsomewhere. Two circuits are involved I would guess the auto one and the switch one, separated by a diode or two to prevent feedback into the other circuit? I really am just stabbing at answers. The switch circuit has got to be pretty simple.
The limit switches must alter the motor direction when reached, maybe just a switch problem?