Lottery officials this summer seemed shocked to learn that a handful of high stakes gamblers had taken over one of their $2 games, with just three betting clubs accounting for most of the winning tickets statewide during periods when prizes swell. The lottery disciplined two sales agents who allowed the high-rollers to run the ticket machines themselves and announced new rules. But, a Globe investigation has found, lottery managers have for years allowed and encouraged the groups to manipulate the game, Cash WinFall.