Most our plug-ins will create popup Windows to let the user enter values or change preferences. It appears that when the “Always On Top” feature of Cubase is enabled, all our non-modal popups appear behind the plug-in editor, so users cannot interact with them.
After spending time debugging this, it appears that you are not using the standard WS_EX_TOPMOST window style for this feature but something else that keeps bringing the window to top when some new windows are activated (we keep getting very strange z-order behavior as soon as child popups are created).
Can you maybe tell us more about what this option is doing so that we can find a workaround? Is there maybe a way to detect when this mode is on? Any hope that you could simply use the WS_EX_TOPMOST window style instead?