From my experience, route following mode only works well if you also engage altitude hold. This is different than Su-25T where route following automatically maintains the programmed altitude. This was true even before this update and it didn't change in this respect. It's like in Su-27 route following mode is a lateral mode only. When altitude hold is engaged while route following is in effect, it maintains programmed altitude (instead of a fixed one when used standalone). Is this what you are seeing too?
(Ironically, I think our beloved Su-25T has the best autopilot in the game...)