AIR internal windows become visible?

We have an application that hosts the Flash player to run SWF movies and occasionally launches Windows executables when the movie asks so through an ExternalInterface API. This has been working fine for several years now, but recently it was brought to our attention that using it to launch a program that happens to be a Flex/AIR executable containing a browser object causes one, two or three internal windows to pop up and become visible; their titles are things like Msg, SWBrowse and _acroS_win.

When running the AIR executable standalone, those windows do not show up. Inspecting the process shows that they actually exist but they're hidden. So it seems that something in the AIR runtime decides that the windows should actually be visible when launched from our application.

Hints/suggestions as to why those windows pop up or how to prevent them from doing so are welcome. In our tests so far, using another program that doesn't host the Flash player to launch the AIR program helps only for applications built using Flash Develop and the AIR SDK. If Flex is used, the windows always show up.