I have somewhat of similar problem.
Additional to the case, that it does not recognize my Joystick in-game sometimes, i have also problems that, even the Joystick responds i did not have any Force Feedback effects.
Sometimes i have to restart the game three or four times to recognize the Joystick and to get the Force Feedback effects.
But i have to say, that i use a nightly build, maybe the one with a new Controller input?
I do not think that this in an error in the launcher, because i still use the outdated FS2 Open Launcher 5.5g, that afaik use the same configurations like the wx one.
But it seems that FS2_Open did not recognize "Spring Center" at all for a few versions, even all other FFB Effects are there.