I've got the same system. When you say manually put it in I assume that you used the bars to turn them in manually? Did to try the bypass that puts the wall controls for the motors to "only in"? There is a small reset switch on the back of the controller (you have to unscrew from the wall and it will be toward the bottom back of the control board) that when pressed for about 5 seconds will start the red lights flashing in unison. This then transfers one motor control to each button (both in and out will control a different motor but only bring them to the closed position). I've got an issue with my front slide and have to do this every once in a while. I am not sure the solution and will need to get it into service at some point (but haven't had the chance)
2010 Winnebago Vista 32K with a 2013 Mini Cooper S Roadster toad.