I've received this message multiple times and the only way around it is to completely export everything into a new scene = pain in my ass. This error comes up when I go to the render to texture options and start picking the high poly elements to add to the projection. Once this message comes up I can't even select any render options like turning of ray misses for AO maps.
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Does this happen with a completely fresh scene and new test-objects, too, or can you link it to certain scenes? (I guess what I'm asking is: How unpredictable is this exactly? )
Try to deactivate the autowrap if you add the projection modifier manually.
(First add something foolproof like a box and then reset the cage and deactivate the autowrap before you add more complicated geometry. )
Have you done something like that?