If the nested groups are really nested within the root group node, then this should not happen at all. Also, it shouldn't be neccessary to use the "Lower Selection" in the first place, since nested structures are by default painted in proper order so that the nested elements are always on top of their containing elements.
That said, are you sure that your root group node really contains your nested groups? Or do they only happen to overlap with it?
You can test this, for example, by moving the nested groups around. If the root group node resizes as the moved groups approach the border of it, then they are contained. If you can move the nested groups beyond the border and the root group node does not resize, they weren't nested in the first place.
(Alternatively, you can also just have a look at the object tree in the Structure View to see whether the nested groups are on a level that is more indented than the level of the root group node... :-)