I noticed several errors for the AI Ships as well. Most of them harmless, but three of them might result in unexpected behavior in FS9.

For motorboat_medium, there are indeed two fltsim.0 entries. I'm not sure if this is a problem. Perhaps the second one will be ignored by FS, it might not show up?
For sailboat_medium, the aircraft.cfg file says "white_nosail" as model for fltsim.3, but the model folder is actually "white1_nosail".
And for sailboat_small, fltsim.2 asks for a "red_nosail" model, but the only no sail model is "white_nosail".
I think those last two will indeed result in a couple of no-shows, right?