Corner window is the same window, just driven by Add-on. This is very old Add-on - since version 6.5. It behaves the way, that when you place corner window, it creates second one and connects their parameters. So anything that is not length will be reflected in second window. So, when you change mullion height - it moves in second window too. But as soon as you move one window away from second - connection disappearing and they are becoming two independent windows.
Before this tool been introduced in ArchiCAD existed very simple solution - called "Custom Corner". It's available as for simple windows as for corner.
Just use two Independent windows with custom corner switched on. Then you can modify one window, and second is not going to follow this change.