<i> The way I have wrote it causes the windows to lose and gain focus as expected.=A0 Does anyone know how to stop the focus from constantly changing?=A0</i><p> The focus is changing because the execution is changing (in the same thread). You have the VI with the graph execute, and then quit. This will lose focus.
My occurrence-based scheme had all child windows executing at the same time (different threads). This meant that the window on top had focus - no other window would have it until you clicked on that window (and brought it forward). Hope that helps.