Really, I think it comes down to being one of those things we'll never know and tbh I don't really need to know things like that.
When it gets down to it, if you work very closely with someone for a long time, there's bound to be differences of opinion which can flare up. A football coach and his captain basically live in each other's pockets... so you'd have to think there would never, ever be a 100% successful friendship with no disagreements or tension between any of them.
tallis said something in an interview once to the effect of that for him wayne has lost that sort of aura around him (everything wayne says is gold type of thing) to him after the whole rooster's deal...it was something like that he said he still respect him for his place at the broncos or whatever.
Agree with Mick, it is just bound to happen, doesn't mean they are not good mates and what have you, obviously they just dont see eye to eye on everything. Both going their separate ways also, probably meant hey didnt have too much contact post retirement.