The TES can reveal that Eton College is among schools to have contacted the Qualifications and Curriculum Authority (QCA).
The independent school, which both Princes William and Harry attended, has presented the watchdog with a dossier of examples, including two pupils who were given zero marks in a Russian A-level paper, which were then changed to A grades after being re-marked.
The QCA investigation will ask whether exam boards could improve the data they use for checking that marking standards have been met. A review is being carried out into how the awarding bodies handle inquiries about results and appeals. The dossier from Eton outlines feedback from both GCSE and A-level subjects.
The school put in 711 requests for re-marks of last summer's exams. As a result, 11 per cent of those papers were changed.
An Eton spokesman said: "That 11 per cent of those we asked to have re-marked had changes made in grades seems to us to indicate there are major deficiencies in board practices."
Latest national figures, for 2006, show that among nearly 7 million A-level papers taken, only around 0.1 per cent had grades changed following a re-mark. For GCSEs, the figure was around 0.18 per cent.
The QCA began its investigation late last year before receiving the Eton dossier, but after complaints from some state schools and several leading private schools.
Haileybury School in Hertford and Epsom College in Surrey had nearly half of their pupils' English GCSEs upgraded in 2006 after appeal. Isabel Nisbet, QCA's director of regulation and standards, has written to union leaders saying she is aware of teachers' concerns.
The authority had convened focus groups to examine the issue, she said, and it intended to commission a survey of school and college views.
It would also be exploring whether exam boards could look at data on pupil performance across a whole school, before issuing results, to help spot odd patterns.