Since Creo 3.0 the workflow for paste special with advanced reference configuration was chaged. If the reference dialog for the paste action appears it is behind the active window at the beginning. If the user clicks on the reference selection window it comes to the front. When moving the mouse pointer above the reference of original feature area the original window (where the feature was selected) comes on top. The reason for that is to have the original model visible where the feature was copied from. This was changed because of an user request (see Article: CS287471). That behaviour ist not very streamlined and the current workflow is to make the Creo window of the source part smaller to have full access to the dialog.
The idea to change that would be a second window that should appear inside the target window showing the source part. The same behaviour as it is when selecting references for copy geometry.
