This could be a problem with your transfer switch contacts. One of the contacts is not passing voltage through from both hot legs of the 50 amp service. The same thing happens with 30 amp service just that the total usable amperage is less.
I would guess that you either have a failed broken transfer switch or a broken wire connecting ti to your main panel. Also you do not want to overlook the possibility that your main 50 amp circuit breaker is bad. this would be in your main circuit breaker box. You might try resetting it.