This is a known bug in SDL 2.0.9, which is already fixed in the hg code, so it will be fixed in 2.0.10, see https://bugzilla.libsdl.org/show_bug.cgi?id=4391 - a short(-ish) explanation of the bug can also be found at SDL2: lag with SDL_GetTicks
A workaround is to add SDL_INIT_JOYSTICK to your call to SDL_Init() (yes, even if you don’t want to use any joysticks and don’t even have any connected to your PC).