It’s a little hard to tell from your description, but it sounds like the coordinates are being set as relative to their parent, but Stardust (?) is based off these coordinates.
If you have a 3D Null object at 960, 540, 0 and you have a 3D solid also at 960, 540, 0. If you parent the 3D solid to the Null, its coordinates becomes 0,0,0.
You might need to use an expression like in the Stardust effect’s position property. This gets the coordinates of Null and bypasses parenting.
L=thisComp.layer("Null 1");
L.toWorld(L.anchorPoint);
http://www.YouTube.com/ShiveringCactus – After Effects Tutorials