Mine has the same problem (bought used on E-Bay) the window was not sealed in the door. The PO or the dealer put plywood down and rebolted the step BUT didn't correct the underlying floor so I will have to remove all of it and find SOLID area to start from. Your best bet is to remove the wood and look for solid and replace all the wet and rotten wood.
1996 GulfStream Conquest 31feet May 2011
1984 SouthWind 27feet loved for 6 years
1 Wife 6 Kids