Are you running them with the CH Software mapped?
I have tried disabling and enabling the Steam-Cloud setting and while it seems to delete all controllers and assignments, it still does not allow the game to pick up the axes
.
When I clich the Clear box followed by the change box a new box pops up which like the old IL2 46 is meant to pick up on any control you move, however absolutely nothing happens.
I'm stumped but I'm sure it's a simple tick box somewhere I'm missing.