Just so you know this is a problem on every game. I use two 17" LCDs and every time I start a game (Any HL based game like CS, HL, HL2, CS:S, CS:CZ; or MMOs like World of Warcraft, Sword of the New World, Guild Wars, etc) and run it in full-screen mode, it changes my resolution on my second monitor and puts windows half-way off the screen.
Sure, but JOGL does not do this to me… (leave other windows messed up when I quit full screen mode.) Maybe just due to a different way they do windowing or something like that.