Maybe your timing got moved sometime and it is a little retarded.I've put a good battery in mine so many times I've lost count. That system stinks. Polaris knows it as well. They admitted as such to the dealers when they sent a letter to us saying we didn't have to order any RXL or EFI 500s because of all the issues they had with them. They would understand it if we the dealer did not want to sell them anymore and we didn't.
I've got the software, I've got the hookup for it. I've even used a Polaris EFI tool for it since I know the guys at Polaris up here and nothing comes up wrong and yet it runs like garbage all the time. Doesn't matter what we do it never wants to idle right, doesn't matter if we have put in new injectors, new filters, fuel pump and so on and so on and so on. I am trying one last thing and that is the fuel pressure regulator as that is the only part that hasn't been replaced if it doesn't work it is getting junked. Had enough of it and it is a back-up snowmobile anyways.