Re: onan 5500 generator
Unless your transfer relay is very different than any that I have seen, the batteries will have no effect on it since the power to it is 120V-ac. What make is the transfer relay? If you can give a brand and perhaps a model, I might be able to locate a schematic for it.
Most transfer relays are designed to default to the shore power position when there is no power at all to the device. The coil of most is connected to the supply that comes from the genset, so that if you are on shore power and start the genset, once voltage is available from it the device will transfer all loads to the genset. This is a good design, as long as the owner remembers to always shut off all significant loads before they start the genset.
Transfer devices can, and do fail. To me it sounds as though yours has burned contacts. You can open it to see what things look like inside, but before you do make sure that the genset is not running and the power cord is not plugged in. If the power has been transfered under load, the contacts can either become burned to where they do not make good contact, or they can even weld shut in one position.
An easy way to check this is to connect shore power and make sure that you have 120V to the outlets. With nothing but perhaps a small night-light connected and operating, start the genset and allow it to warm up. If things work properly, you should now be able to open the circuit breaker at the power pedestal and the light will remain on, indicating that the supply did transfer. The catch is that since this is an intermittent problem, it is very difficult to be completely sure. A look inside of the transfer relay might be a good idea.
Of course, if you are completely sure that there is no voltage at the genset side of the transfer device when it is running, that would indicate that the problem is the genset, but I would take a very hard look at the transfer device before I went farther.