Window is transparent sometimes but not always

I've been trying to replicate the messageWin little popup messenger from the kitchen sink. It works perfectly when over my initial log in screen. When I call it from my main window it shows with a solid white, non-transparent, background taking up the whole screen until the timeout runs it's course. Here is the code I'm calling: http://pastie.org/1485466 which I call with:

Ti.App.fireEvent("message",{page:'main',msg:res, wait:5000});

Any ideas as to why it will have a transparent background when opened during the login but not when opened during the main?