Musoke

Do you have multiple monitors?
Try to maximize the Query editor window, see if that will show the tables window?

Yeah, that's a weird one. Or maybe try scrolling around inside that table area inside the query, where you see the horizontal and vertical scroll bars. Maybe they're getting placed off to the side somewhere. I've never seen that happen before, but it's possible. I know the global relationships window can do this sometimes - it actually keeps track of where you save that stuff. If you move it to the right or far down to the bottom, you won't see it next time you open up the window.