OK this is my last question, I promise

I have connected up my J-PAC, everything seems to work fine apart from the bottom 3 buttons on the second player. The left most one works but the other two do not. (This is buttons 4,5 and 6)
I tried connecting them up to the connectors on the J-PAC for player 1 4, 5 and 6 and they all work there, I have tried connecting player 1 connectors to the player 2 4,5 and 6 and they dont work there..... (basically anything I plug into the 2SW5 and 2SW6 connectors on the J-PAC dont work)....... does this sound to anyone like I have a faulty J-PAC? I am running advancemame with the default settings for the controls, and I think that this is all OK as the Player 1 controls all work OK.
I really appreciate the help people, I dont really want to have to send the J-PAC back as it takes a while to get there and get back to me here, but will have to if thats what it takes.
I hope that this all made sense

If there is anything I missed please ask and I will provide it.