For some reason NesterJ keeps deleting all my games at random times when I use it, it sucks :'(
I will wait for final version of this so at least SNES stays intact.
Strange, I haven't had that happen to me before.
So far the only problems I've encountered with the new SNES9x is that you can't put the system in sleep mode and depending on the engine you have set you won't be able to use the HOME button to go back into the GUI (though I found holding L and clicking Start to switch modes fixes this).
Most of the game I've tested work great now and the ones that gave me serious issues before work fine when you set the Engine to Accurate and the Frameskip to AUTO. Mode 7 games still run like ass though.