Ok so here it is,

Before Jane answers the phone(in season 6 episode 1) he talks to Ron and he ask him if he has seen Lisbon and if you look closely Ron has a phone in his hand and when Jane turns his back he gets a call from "Lisbon' but its red john. So I think it was Ron who called him because when red john says sorry Jane she cant answer right now he has his 2 hands busy one holding the knife and the other one cleaning it. That scene happened before the call. Heller is just trying to confuse us. He wants us think to think its not Ron but it is! He called Jane right in front of us! 

Thanks :)