When clicking the close-button on a popup in our application, the server sends a new site which contains only the javascript which should close the popup. The framework seems not to like this method of closing a popup and closes the main window too.

The workaround is to remove the popup from the browsers collection after the Click:
closeBtn.Click(true); 
manager.RemoveBrowser(popup.ClientId);

To reproduce:
Sample project is attached to the internal bug description.