Rotating sub-assembly during insertion into top level assembly

When I try to rotate a sub-assembly "B" after I insert it into a high level assembly (which already has sub-assembly "A" in it) - the parts of sub-assembly "B" (which is a copy of "A" - I just want to rotate it) change position relative to other parts of sub-assembly "B". They "fly apart" to some extent and that extent depends on where the center of rotation is. I want the relative positions of the items in sub-assembly "B" to stay constant. The purpose can be thought of as the top level assembly is composed of two sub-assemblies, each of which is an assembly of two adjacent sides of a box (with other stuff attached). The result should be symmetric across the diagonal of the box.