Pupils are twice as likely to have their A-level grades changed on appeal if they have taken their exams with one board over another.
A-level hopefuls who appealed to AQA last year had a one in eight chance of having their grade altered, as opposed to a one in 17 chance with OCR.
This shows yet another inconsistency in the supposedly standardised exams system, according to Anglia Assessment, the independent education consultancy that has been tracking the two boards for the past six years.
George Bethell, its director, said: "While the gap at GCSE is narrowing, at A-level it is getting larger and there can be only two explanations: AQA is less reliable, or something happens within OCR to resist the temptation to change grades."
He added that there would always be discrepancies in assessments, but you would expect to see a similar pattern across the UK. However, pupils were not necessarily better off with AQA because it changed procedures frequently.
"You have to ask why AQA is making so many changes in the first place," said Mr Bethell. "If you award a student a grade and they appeal and the grade is changed, it shows an error has been made and that can dent public confidence."
AQA said it was company policy to "apply every mark change, however small", so if a mark was close to a grade boundary, the candidate would move into a different band.
A spokeswoman said: "The marking of our examination papers is a thorough and rigorous process, which is carried out to the very highest standard. The overwhelming majority of results issued by AQA are correct, which, we appreciate, will be of small comfort to the individuals who were initially issued with an incorrect result."
They were always looking for ways to improve, she said.
OCR said Anglia's claims were "backed by little evidence", but added that its grade changes were low because of better standards.
"The past few years have seen huge improvements in OCR's ability to recruit and retain first-class examiners, and we have spent much time enhancing our management and training of examiners," an OCR spokesman said.