Emulator

Sure. I set correctly. It works with other game. Only ToS can't click at menu
previous version works with it. (around r1000-r2000)

I use psx pad. This is my setting.
http://img131.imageshack.us/img131/8532/sshot1m.jpg

Anyone else having problems with this?

It may be something with your framerate: sadx has a bug where if the framerate drops
below ~45 fps, you have to press buttons several times for them to work.

Your configuration looks fine...
Does it work with the keyboard plugin ? and can you please try with an earlier rev
like >r3106 ?

ok. I already update my dolphin r3140.

Test njoy with keyboard : Everything works fine.
Test dolphin x360 plugin : Everything works fine.
Test njoy with my pad : Can't press at menu.

did you try renameing sdl1.3.dll to sdl.dll? could be that sdl 1.2 doesnt work well
with your pad

I tried all sdl 1.2 and 1.3. It same.

Only button don't work. Main stick and direct input work.