I have not worked with a 50 amp setup. You say you have 2 transfer switches, each in a separate box. Maybe someone will chime in. I wonder if they split the genny output into two circuits and send the to the two transfer switches. You said everything works on shore power, so means the AC breakers are OK. Did both relays flip or just one? You seem to be missing 1 hot leg from the Genny. If you studied my photo you could see that I had a bad wirenut connection on both wires from my Genny and it melted the wire nuts off just like a kid with a marshmallow on a coat hanger over the fire. If you are comfortable working on this stuff you could examine the splices coming in from the Genny with a meter, or at least look closely for any tell tale signs that you have a connection problem.
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