I would start checking the main breaker in the panel, see if you have good power entering the panel from the surge protector to the main, both legs. Also check the neutral. All connections tight and not arced. If they get loose, they can heat up and cause arcing and can damage the main breaker.
As far as the Gen disconnect box, I'm not sure if the main is wired into it first and then to the main panel, if so, then look at that. It could be an issue inside it. Loose connection etc. The Gen protection is suppose to cut shore power if the genny is powered. So it may be the issue.
Just a few things for ya to start with. Good luck.
Bill
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