This is exactly what happens to me. I've been able to work around most cases by pausing the SKView and not the SKScene. This fixed the issue in my game when a user paused or left the app. However if the user dies and start again, it still randomly goes to 40fps. Pausing and unpausing brings it back up to 60fps.
The instance where the user dies, I used to have logic to reset the scene. I tried switching my logic to recreate the scene every time, and it still can randomly drop and get capped at 40fps.
Its hard to say, but there seems to be issues with the physics engine running while a UIView animation is happening. For instance we have a view on top of the game scene. If I unpause the game and start an animation to alpha out the over top view at same time, it drops to 40fps randomly. If I wait to unpause until after the animation, it never seems to drop to 40 fps.
I also know my trick of pausing and unpausing to get the fps to jump back up to 60 does not work if I only pause and immedately unpause the SKView. However if I let my pause view aniamte in and out between pausing and unpausing the SKView, it's fine and comes back up to 60fps.
TL;DR - try to only pause/unpause on the SKView level and do not animate via UIView at the same time the pause toggle to NO happens. These seemed to do the trick for me.
Edit: Still seems to drop to 40fps randomly, though the amount of times it happens is significantly less. Least I can continue to develop until Apple gets a fix out.