Winchester College, in Hampshire, lodged an appeal after its sixth-formers received very poor marks for an assessed project that was part of the 1997 exam.
Some candidates had failed their project modules - even though they were given A grades for all the examined modules.
Five students' project marks rose by up to three grades after remarking, but the school remained dissatisfied and complained to the exam watchdog, the Independent Appeals Authority for School Examinations.
The watchdog upheld the complaint, saying that there was too great a discrepancy between candidates' project grades, predicted grades and marks in other exam modules. It concluded that the board's marking had been sub-standard and asked it to review its procedures with the supervision of a senior examiner.
The project required sixth-formers to investigate economic issues. But students often chose topics that did not lend themselves to this kind of analysis, the independent examiner found.
He had serious reservations about using this type of assignment as a means of assessment. The watchdog praised the board's tightening of procedures for approving project titles, but urged it to take the independent examiner's wider concerns on board.
Michael Fontes, head of economics at Winchester College, said: "We cannot understand why the boys' project titles were accepted by the board in the first place if they were not titles which could get a decent mark, especially as they were so similar to sample titles sent out by the board itself."
A spokesman for the board said: "Most of the IAASE's report exonerated what the board had done. The investigative assessment was a choice and Winchester College had not chosen this option before. The panel agreed that the candidates had not chosen appropriate topics for the assignment.
"In the light of this experience, schools would be wise to look closely when they take this option.
"But it is a popular option and most candidates score highly on it."