There seems to be a bug when you create a sub application at runtime and use "Popoup Window" & "Modal" and use Create at XY of an Object.
I tried to create the object exactly next to another sub application and later switched to a active just to make sure its no problem with the sub application. If you untick both options the sub application will be created at the correct position, even if you scroll around it works perfectly. Once popup & modal are active it goes way off. On the top left side of the screen its somewhere way below the actual position and it changes location around if you try it on other places on a scrolling display.