There is no indication that Flatcar decks were painted. Same with inside gondolas, inside boxcars, etc. These areas were expected to be abused, so the wood was considered sacrificial. As long as it protected the cargo appropriately, it did it's job. That is alson among the reasons why the railroad had so many carpenters in the car shop.
Also the underside of the cars wasn't painted. Just raw wood that aged and weathered. These areas would have been a real pain to paint in the first place. Also, the water didn't stay there, just fell off, so no real reason to protect the underside.
Phil Hackman