It should be working a lot better with how sloped/corner blocks now have full drag effects (but still no/little lift it seems).
Also, with the pressurization update they added error to buoyant crafts to get bounce and such to them (which reduced server load as well as increasing precision), this effect also applies to things in the air abet to a far smaller effect, but enough that any stability you thought you had, this tiny bit of error will throw it off in a big way.
As I pointed out, the space shuttle has a comically large rudder - it's larger than it's own delta wings. This is how, in real life, the space shuttle can maintain attitude at hypersonic velocities.
There were a lot of craft that relied on the game introducing no errors into their flight characteristics, unfortunately your craft was among them. That is to say if they added weather or anything else, your craft would have destabilized because there is so little rudder control for the wingspan.
I'm not trying to be mean or coarse, but the only reason your craft flew straight to begin with is because the game never threw your craft a curve ball as it does now, your craft relied on the 0-error system it once had. But this also means that no one has a craft that seemingly "flies on rails" any more (not even my own). There is slight deviations in flight characteristics that players and autopilots have to deal with to keep it flying straight.
The only way Batch could rectify this is to roll back the deliberate error introduced in the pressurization update, and forgo the introduction of weather. I'm sure you wouldn't want your craft to fly straight at the cost of never seeing weather in the game.