Lloyd said:
2. When I first click on a pink gear to do editing etc, the top of the popup menu is off the top of the page. I have to click outside the menu and then click on the gear again to get the popup menu to appear in the right position.

I think that this only happens when clicking the action menu icon in a sub-window. So the sub-window click event doesn't know that it's in a sub-window until the second click?