First note the last post in this thread stating CS6 is not compatible with 10.8 Mountain Lion:
This may or may not be related. Do you have an example to verify if it's also a problem on Windows? If Windows does not exhibit the same behavior then it very well may be a Flash Player or CS6 incompatibility.
What are you setting the stages display mode to when you run the SWF or projector? Is it fullscreen by default?
Interesting to know about 10.8 and Flash. I'll hold off upgrading until they work together. Currently using 10.6.8 at home and same on the Universtity's computers.
Haven't verified on Windows but shall do later in the week if I can get access to a Windows machine.
Both the Flash player and the Projector come up not full screen, and if I leave it that way then things work OK as long as I don't make the video full screen (using the full screen button on the skin).
However if I make the swf or projector full-screen (by using CMD-F or the menu option) then when I click on the menu item to take me to the page with the video on it, instead of a page with a smallish video and back button I get a black screen with no obvious controls. If I then press Escape I get my normal screen back and I am in the page that should have the video but there is not video and the back button does not work. So something wierd is going on here.
If I make a file without any videos with a similar navigation structure everyting works ok except that when I go full screen I lose the finger cursor when I roll over my buttons (which is also wierd).
What are you setting your stage scaleMode and align to? if you dont set them then the stage may be growing in a way you didnt expect, pushing controls off screen.
If you make a simple sample project that fails in the way you describe I will test it on Windows and let you know if its reproduced.