I was having that problem with setting up Mode3. I would select that mode while in mode1 and had no end to problems with miss matched keys. If I wanted to setup Mode3 I had to first change to that mode then use the configure controllers app to reassign buttons. I kept closing my clipboard every time I tried to setup one key in Mode3 until I changed to Mode3 first.
I've gotten everything to work along with having alternate buttons for CM-Eye in Mode3 for terrain work. I did discover that the 16in guns really want to start from about 10,000yds before the hash bar in sea mode will aim correctly when you set azimuth using the new keys. The 5 and 8 inch allow for closer ranges. Oh, and set your target to 1000, 360, 12 then adjust the iron sight for the 37mm so the top of the vertical fin is dead center on the target when you are hitting dead center with the horizontal bar level with the red horizontal line of the target. I don't know when the last time Hitech or Waffle set that thing. I even adjusted my wirble reticle to center at 1000 since most of our shooting is between 1000-1500.
