If you had a ground issue on #2 battery, I would not expect it to be able to start the boat. But, never hurts to check grounds. I would check to see if the alternator is indeed not charging the battery, maybe the battery is just bad again. With the engine off and the shore charger off, measure the voltages on both batteries at the battery terminals. They should be ~12V. Then select #1 and start the engine, measure the voltages on both batteries at the battery terminals. If it is being charged it should be about 13.8V. Repeat for #2, the charging battery should be at 13.8V. Repeat for ALL setting, both batteries should have 13.8V, although this could be slightly lower as the alternator may not be able to handle both batteries in parallel. If you notice only one side is getting the 13.8V, check where the alternator is connected to the battery system. Someone could have placed it only on the #1 side. It should be after the #1 / #2 switch. My FourWinns has an isolator, but the manual for yours did not mention one.
The manual
http://www.fourwinns.com/uploads/2017/2 ... downer.pdf
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2010 Vista 338 Volvo Penta
2005 Yamaha Wave Runner FX HO
2005 SeaRay 280 SunDancer
2001 SeaRay 245 Weekender