I got the same problem as ever.
I believed the native pad support would have fixed this
when i use 2 controllers on the sixaxis tool (as native pads) on my GT-9300 S3 and set the keys for both of the players in FPSE, both controllers controls the 2 players at the same time, i can't have fpse know that even that they are the same button config, is for 2 different controllers.
fpse just recognises 1 set of keys as the same controller, cant differienciate pad 1 from pad 2,
i dont get this problem on any of .emu emulators (nes snes etc) just so maybe, you can check them out and see if you can have a similar way to fix this, the snes one is free at his site:http://www.explusalpha.com/home/snes9x-ex/downloads