Well I got a simmilar situation going on but in my case windows minimize when I click my popup shortcuts.
So having said that. You could
*jDeskMButton1 [.none;!none;!Your on-close actions;!none]
so when you click the desktop to make your popup disappear you get your on-close action.
offcourse if you actualy open something with the popup,you dont get to click the desktop or your !on-close action.
maybe you could work the problem from there.
like tasksOnAdd to make sure your on-close action happens if you open something from the popup.

I think you meant LiteRunner not One.