I'm working from a computer running linux kernel 2.6. I checked out the code with svn a few weeks ago; the 'About' file under Help says it's version 1.2.11. I built JSwingBoy with Eclipse 3.4.
In-game, any attempt to click File-->Save Snapshot or use the 'ctrl-alt-S' command resulted in an error window containing the message 'Failed to save the emulator state!' (see attached screenshot1.png). The game shown in the screenshot is EggRacer.cbg, as included in the download package. I also tried this with CrazyZone.cgb and Drymouth.gbc, with the same results.
Whilst the error message displayed, the game continued to run in the background, but interaction with the game was impossible whilst the window was displayed. In a game like EggRacer, where constant participation is required, this lack of pause caused me to loose the game.
If this is a case of a planned enhancement that has yet to be implemented, perhaps it would be better to remove the 'Save Snapshot' option from the file menu until it's needed?