For some reason one set of my counter measures will stop working only allowing me to either use my chaff or my flares and the only way I can find to fix this by changing my plane
Have you checked so that you don’t have the “switch countermeasures” key bind on something that you might accidentally press?
Or check the on screen weapons selector hud where you can select to drop only chaff or ofnly flares?
I also have this issue, and to cover what necronomica asked, both chaff and flares were selected but no flares would release after the first press while chaff would continue to release. With only flares selected 0 counter measures would be released. Using my own keybind or alt+e yielded no change. Im not sure if it is a general problem or if it is only the f4 in the event, but like the original poster said, playing another vehicle and returning to the f4 is the only way to fix the problem.
I have had a bug a couple of times now, it seems to happen when I have been destroyed right as I activate my periodic CMs and then respawn the same plane, it locks out the CMs completely. It’s not a key binding issue, I have cycled through the chaff and flares and also tried the keys I have bound for individual chaff/ flare launches and even tried using the multi-function menu to launch them, they are completely blocked.

