The election, which cost over Pounds 1,000, resulted in a substantial victory for Howard Phelps, chair of governors at Cirencester College, over the runner-up, Margaret Morgan, chair of Southwark College.
The AOC was formed from the merger of the Association for Colleges and the Colleges' Employers' Forum. Mr Phelps' success was widely seen as a victory for the former CEF lobby, as tensions still remain between the two groups.
The college heads who say they were not balloted appear to come from former AFC colleges. It is understood there was a genuine mistake over the lists used for the ballot. But any suggestion of impropriety would be deeply damaging for the entire leadership.
Roger Ward, the AOC's chief executive, said: "If there is a complaint with any whiff of substance in it, I will press the board to re-run it."