The function you're looking for is nativeWindow.globalToScreen(), see: http://help.adobe.com/en_US/FlashPlatform/reference/actionscript/3/flash/display/NativeWin dow.html#globalToScreen()
Again, this function is dependent on the application's implementation, so like what you've already seen with x/y position, its support will vary between applications.
Thanks, I should have mentioned that I had tried that too. Same result when using these:
nativeWindow.globalToScreen(new Point(x,y)) );
nativeWindow.globalToScreen(new Point(mouseX,mouseY)) );
stage.nativeWindow.globalToScreen(new Point(tabNavigator.x,tabNavigator.y)) );
Again, in Illustrator the above code works fine, in Premiere it always returns (0, screen y resolution).
Any other ideas are very welcome, positioning a window relative to another one should be a pretty basic part of the api.