It has been a long time since this post hasn't been active, but since i didn't find anywhere else to post and since this bug is still bothering my game experience.
I have seen this bug since 2.5.5, (when i bought the f-14), and it's still happening in 2.5.6.
I'm using TM Warthog stick and throttle and TM Rudder pedals.
I've found that to me the conflict is happening whenever there is only 1 throttle axis mapped ingame. Then my Rudder axis goes red.
So as i wanted to have the axis "Throttle Both", i just mapped Z axis of the TM Warthog throttle in it, and mapped RZ axis to the "Throttle left" then tuned this last axis to have 0 saturation.
In this way there is no conflict anymore, and i don't need to change game files.