I'm not sure why, but on a fresh install of freebox aka e-touch when I went to run full screen on a 1024x768 skin I would get a small window with some of the content removed. It was like a cut out of the screen with some of the buttons visable.
Ok, to fix this run 800x600 at full screen and exit.
1. Find you freebox.ini
2. Find [Current Skin]
3. Change from Black_and_Blue_V5_2 (800x600) to (1024x7680)
4. Restart freebox
Now I've only done this with a single monitor running 1024x768 on full screen.
I have had this problem too. I find it starts up default in 800x600, so I go to the options and load the 1024x768 skin, which results in the same problem as you.
To fix it I just click on the 12 covers (or whatever it is), then click load skin again and it works. though maybe just loading the skin twice would fix it too.
I too have seen this and i'm not quite sure what causes it so it's quite hard to actually fix because it doesn't happen all the time. I will try and see if i can fix it for the next release as it is annoying.