I'm using ZSNES 1.51 on Ubuntu Hardy, playing with a Logitech Cordless RumblePad 2 (P/N 862350-0000)
Whenever I play for a certain ammount of time (I can't figure out anything that might cause this besides time), the game leaves full screen suddenly and my keyboard and mouse stop working. My controller still works, but I have to Ctrl+Alt+Backspace to get keyboard and mouse functionality back. I can still do things like switch to the terminal with Ctrl+Alt+F1 and back to the gui with Ctrl+Alt+F7.