HHH and Jim Ross are good friends and whenever you see him back its likely because it had something to do with Jim Ross. HHH appreciates that he is a great commentator that adds a special exciting touch to commentary. He also respects him as a booker and great talent spotter as Jim Ross knows what hes talking about, I believe it was him who spotted and signed The Rock.
On the other hand Vince McMahon cant stand Jim Ross, at every opportunity he gets he humiliates him, in the ring, out of the ring and backstage. He hires and fires him all the time messing him about, then when he does bring him back its usually to humiliate him.
I think the reason VInce doesn't like him is because he feels so threatened by him Jim Ross is multi talented and has done some great work as a booker and as a commentator. VInce doesn't like anything much that wasn't his creation hence the reason a lot of the WCW roster was buried and the reason Sting never jumped ships.
All in all the way Vince treats Jim Ross is awful.
When HHH takes over more maybe we shall see Jim Ross more.