The problem is most likely that you have your devices arranged in a non standard way.
Normal is G940 Joystick on ID1, Throttle on ID2, rudder pedals on ID3. I think you have your rudders on ID2 instead of the throttle. This is why when you press the toe brakes of the rudders, the program thinks that is the throttles.
Two possible solutions:
1. You get the JOY ID changer tool from
www.wingman.com and set them in a standard way. But if you do that, most of your control setup will probably be lost in IL-2 (and all other games too), because you already set them up to be in this non-standard way.
2. A probably easier way, you set up the profile in the Multi-throttle program like people who don't have G940 would. Use the joy ID tools included to scan the ID slots (1, 2, 3 etc).
Then you move your rudder, throttle and all that, to see which ID they belong to.
Then you edit the mikkonfig.ini file, and just change the number in the beginning for the throttles and pedals to the ones you discovered with the JoyID tools.
I'm sure that your rudders are ID2, so you should change the toe brakes in the mikkonfig file to "2joy...." instead of "3joy..." like now. But you have to find the throttles
EDIT: If don't forget to change the buttons for the engine controls at the bottom (individual engine start and feather) to the ID of the throttle, if you are using them as well.