I had same problems with my warthog every thing checked out when I tested my config but once in the game! It was very frustrating to track down.I found that some key commands I was having trouble with I just remarked out and the sim assigned the function. ie- I was having trouble with my trigger whenever I shot at something it was like it was on semi couple spurts,I remarked out the spacebar command in my config and then it worked! TK had said something like not double programming the keys but I dont know how you get your other buttons configured without assigning a key command,I was just using the defaults not changing anything.But if you have trouble with a programmed command and it's a default key command try removing it from your config file and see if the program is using the same default key command.