I'm pretty sure its just because of what you have "Frame Skip" set too, cause I had this issue when I was using my older computer. ( Settings -> Video -> Frame Skip: Off, On, Subtle )

Frame Skip either slows everything down too the FPS speed so it runs smoothly but slowly, or that everything runs like normal but you can see the low FPS.

I just forgot if either having it on slows everything down or if its having it on that slows everything down since my computer runs way better than my older one.