In AIR 27.0 I still see what looks like this issue, I've seen it before in the past, when I have a video running at the same time, e.g. a twitch stream on my spare monitor(Source quality through VLC/MPC media player not through a browser).
There are visual artifacts, looks like frames were skipped from rendering , even though the statsDisplay says 1000FPS and stays there throughout, it seems to stutter a lot and looks like 60FPS or less, which I am not seeing in other 2D games given the same scenario.
I tried stage.displayState = StageDisplayState.FULL_SCREEN_INTERACTIVE; in 27.0 too, no difference.
Have you tried a newer AIR version recently? I haven't personally seen a 30FPS cap whilst using controllers(I could be wrong) unless it was in an earlier version of AIR, where it would constantly fire 'device added' and 'device removed' events constantly due to a third party controller(this single issue of many, has been fixed), then, I may have seen this issue.