Legislation 12 years ago created the current Motat structure and included the legal requirement that it involve the founding society.
The combination of professional staff and the society's volunteers led to tension which resulted in court challenges and allegations of criminal behaviour.
Mr Hubbard became a target of frustration. During his time, the museum had constant rises in visitor numbers and developed its aircraft collection.
Acting board chairman James Doughty said Mr Hubbard's departure had no connection with the report, which was being used to help form the strategic plan for the next three years.