I'm guessing that you have screwed your screen update order somehow so that you draw 2D first and then 3D which overdraws the 2D. Be caferul how and in which order you use "update world" and "flip" and other commands like text and copyrect stuff. It is perfectly possible to use 2D on top of 3D - in fact, I use 2D-3D-2D sandwich on my own GUI.
2D doesn't work with my 3D
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