I put a tree in a PopupControlContainer inherited class, and attach to a menu item. This works for .Net 2002 nicely. However, When I compile the very same project in .Net 2003, my popup tree doesn't work properly. If a click a tree node, it is often reported that a different tree node is selected.
There has been some changes to the treeview's selection events logic in 1.1.
In the 1.0 framework, the AfterSelect event fired before the MouseUp event. In the 1.1 framework, the AfterSelect event is fired after the MouseUp event, and this might be messing up your logic. So, this probably doesn't have anything to do with the popup.