If you use the Flash standalone player there was a change in version 9.0r115 that affects how fullscreen projectors work. You should probably find out about this before your clients start complaining.
It's quite common to use a fullscreen Flash projector as the splash screen for a CD. It's also common to open PDF files and other applications on top of these fullsceen projectors.
You can't make a document or application appear above a fullscreen Flash projector without a little help (see Opening PDF files on top of interface on FlashKit) but at least it could be done.
If you've upgraded to version 9.0r115 of the Flash player then you can't do this any more. As soon as you make a call to getURL, navigateToURL or the EXEC fscommand your projector window will automatically exit fullscreen mode and return to windowed mode.
This problem doesn't affect SWF Studio, our fullscreen projectors will stay in fullscreen mode for as long as you want them to, this problem only affects verison 9.0r115 of the standalone Flash player.
The only workaround I can recommend right now is NOT publishing directly to an EXE from Flash using 9.0r115. Instead, publish to SWF format and use an older version of the standalone Flash player to create your projector.
To do this, just run the old Flash player and drag and drop your SWF on it. Then you can choose the Create Projector option from the File menu (see below) and create an EXE from your SWF using the exact version of the standalone Flash player you want.
The projectors you create using the Flash 9.0r115 player will have an icon like this:
Older Flash players use this icon:
If you don't have your old Flash player, technote 14266 contains a collection of links to archived Flash players that Adobe has made available for testing purposes.