I use Winds3 drivers for the ps3 controllers here http://www.winds3.com/en/index.htm. In every thing later than Zsnes v1.42win when I try to change a key it goes right to J03 or crashes zsnes. If I map the ps3 keys to the default keys in zsnes it will work fine.
Also I can change the keys in 1.42 and down fine.
I think it has to do with the game pad having 16+ buttons in control panel, but there is no way to change it as far as I see.