Site in question: http://www.lifeionizers.com/
It is indeed z-index, the script that you're using keeps increasing z-index each time an image changes and when it goes above 10, that's when your menu starts to hide behind it. The solution is to go line 117 in nomoo_suckerfish.css and change "z-index: 10;" to "z-index: 9999;"
Is altering the script out of the question? Rather than setting the z arbitrarily high for the menu, I think it would be better to stop the z index from increasing to infinity.
Ah! I had no idea the script did that. You are most wise, Anatoli, thank you!