If you’re using a linux machine with a full-install i.e. all libraries in their proper place and a nice window manager session running in teh BG, you probably wouldn’t come across this problem. However, if you’re running a linux machine to render a flash interface for interactivity instead of loading a proper window manager session, fullscreen with fscommand probably won’t work. This problem started with flash player 9 r115. When made to go fullscreen, the projector clips the display area to a little square on the top left corner of the screen.
Why does this happen?
After days of trying to figure out why, we had a eureka moment. Linux loads TWM (a lightweight window manager) as a failsafe window manager. Thus, when all other sessions are disabled, TWM loads anyhow (even if the chrome isnt available). If you have TWM installed on your linux machine you can test this out.
Workaround
Use a different lightweight window manager and it works like a charm.
ThinkingCap - plugged in to the head 