This week I had a problem with mplayer on my ubuntu machine. Playing a movie at full-screen would only display it at 1024×768, while my desktop was at 1280×1024. Other XV and GL applications would also only use the top-left most 1024×768.
This was caused by Xorg detecting two displays, the connected Acer TFT, but also a LVDS (Laptop screen). This machine being a server/desktop system, there obviously is no laptop panel, but the gnome resolution applet would tell me there was.
The solution to this problem was to tell xrandr to disable the lvds output. I have not rebooted the system yet to see if this setting sticks (or maybe if that would have solved it in the first case) but I’ll report on that as soon as I know it.
The image below shows what it looked like in the gnome resolution applet (only this time from my laptop as the problem is fixed on the desktop)