In Ubuntu 15.04 (also happened with 14.10) the top panel is always visible even when PICO-8 is in fullscreen mode. I'm not sure if it's a bug with Ubuntu, but for what it's worth, other SDL2 programs can go fullscreen on my machine without this problem (both SDL_WINDOW_FULLSCREEN_DESKTOP and SDL_WINDOW_FULLSCREEN work).

PICO-8 uses SDL2 for window creation, right? If not, ignore that last bit :)

EDIT: here's a screenshot: http://i.imgur.com/eWCNKYM.png

For fullscreen mode, I'm manually setting up a stretched borderless window rather than using SDL_WINDOW_FULLSCREEN_DESKTOP, as the latter causes other issues on my dev machine. I'll add it as an option in config.txt though to see if it helps.

sdl_window = SDL_CreateWindow(codo_state.app_title, 
					SDL_WINDOWPOS_UNDEFINED, SDL_WINDOWPOS_UNDEFINED, 
					desktop_w, desktop_h, SDL_WINDOW_SHOWN | SDL_WINDOW_BORDERLESS | 
					SDL_WINDOW_MAXIMIZED | SDL_WINDOW_INPUT_GRABBED);

Yay the new setting in config.txt does the trick. Thanks!

This fixed my fullscreen problem in Fedora 23! The window wasn't centred and part of Pico-8 was cut off. See the screenshot here: https://imgur.com/BXxturf

Setting "fullscreen_method" to "1" in the config file fixed this :)