I am clearing one screen to red, and the other screen to blue, without drawing anything else except the background (so I know it won't draw too slow). I can get the screen to stay the same colour without changing at all.

But which screen is which is random, and has no relationship to what values I pass to the SetLR function. In fact, if I remove the call to SetLR it still works exactly the same.

When I do alt-tab it changes which is which.