This is a small bug that might be fixed in a newer version (I'm using FS-UAE Launcher 2.0.1 for Mint 14 x64).
When I add fullscreen = 1 in the Launcher, it is not written to the config file (the .fs-uae file) and therefore will not run fullscreen when I use a desktop launcher to run an Amiga program.
I can add fullscreen = 1 manually but if I make a change back in Launcher and save, it takes the line back out.
Other than that small inconvenience, I am LOVING fs-uae. I registered for this board mainly because I'm such a huge fan of this program.