Whilst helping the OP, I've seen strange behaviour with the options and auto recovery since upgrade to 1.2.8.
I've just renamed my saved games/DCS folder and fired the game up and gone into controls and it's blank. Swapping between the tabs (System, Audio, Controls), it stayed in this state.
I also couldn't turn the in game music down/off without doing the following:
Turn down in game music, click ok (nothing happens)
Go to system tab and do something (change texture map, click ok)
Go back to audio and check in game music is 0%
Click cancel (music stops)
After doing the above, I the go back to controls and it is populated. Selecting A10 Sim, ALL commands, I operate the boat switch with my Warthog and like the OP, only the boat switch forward is picked up. Boat switch Aft has no effect.
I do have Target s/w installed.
If I copy back my old Saved Games/DCS folder, all is working ok.