I had this exact same issue: X55 controllers show up in game, function ok, except throttle movement was not recognized.
My X55 was connect to the computer through an USB Hub. I reconnected the controllers to two seperate USB3 ports on the computer and it now works properly (throttle movement is recognized).
Strange thing is - when connected through hub, the rhino software would show input working properly and it would even work in number of other games - but not Arma3 :/