I’m also having this strange bug when I finally upgraded to SDL 2.0.6. This behavior didn’t exist in SDL 2.0.5 and earlier. I was wondering why my screen looked distorted after reverting from Full Screen Desktop mode. Each time it happened, it shrunk.
My only guess was it started popping up when hints were added in case one used the SDL_RenderSetLogicalSIze function (either using letterbox or overscan).
Edit: This bug has now been resolved in 2.0.7.