If what OP means is ATP/ITF disagreement, other than a 1990 punishment of Edburg for insulting the "Grand Slam Cup"
1989: Becker vs Lendl
1982: Connors vs McEnroe
1978: Borg vs Connors
The ATP named Borg as Player of the Year in 1978. In 82 and 89 the ATP Player of Year did happen to correspond to the random silly ITF award you are apparently talking about. There were disagreements in those years between the only two things that matter though:
1978: Connors ATP computer #1, Borg ATP Player of Year
1982: McEnroe ATP computer #1, Connors ATP Player of Year
1989: Lendl ATP computer #1, Becker ATP Player of Year
The other thing that matters is slam titles though and that settles the ties in the favor of Borg (78), Connors (82), Becker (89).
Of course this year Nadal was the victor in all of ATP computer #1, ATP Player of Year, and slam titles, making it a blowout, unlike those other 3 years you mentioned.