UV Maps and inconsistent shading issues I'm having some difficulty with a texture sheet I created for my model.  I created UV maps but rotated some 90 degrees so that they would fit on a 4096X4096 Texture sheet. 

Now I'm getting inconsistent lighting when I export. Are all the islands supposed to be oriented in relation to one another?

Not sure why rotating various parts of a  UV maps of a mesh would effect lighting issues.
That indeed sounds strange.
What do you mean with export? As .blend file? To another program?

"Are all the islands supposed to be oriented in relation to one another?" - No except that they shouldn't overlap.

Did you bake your textures previously? (then that might have been the problem, because the lighting is set before you rotated)

Uploading some screenshots or a .blend file might help to solve the problem ;)