But WJEC Chief Executive Gareth Pearce disputes the commissioner's findings and insists procedures have been improved.
More decisions to be taken in 2013 - and the WJEC wants its voice heard.
WJEC's English Language paper was taken by 34, 000 pupils in Wales and 84, 000 in England.
It led to the exams of around 2, 300 Welsh pupils being regraded by the WJEC exam board.
In Wales, Education Minister Leighton Andrews ordered the WJEC exam board to regrade Welsh students' English papers.
Wales' main exam board, WJEC, said last week it had received 1, 000 appeals about English language exam results.
But completely against the trend there was a big increase in entries for the Welsh exam board, WJEC.
The Daily Telegraph's claims led to "an in-depth internal investigation" at WJEC.
For the Welsh examining board, the WJEC, those jagged edges look very much today like the horns of a dilemma.
Students from England will continue to be able to sit WJEC GCSEs - but only linear ones, taken after two years.
The Welsh exam board - WJEC - said it has suspended two of its history examiners and is investigating the claims.
BBC: Government calls for 'fundamental reform' of exam system
They did tell the WJEC to change the grade boundaries but it wasn't their idea - and they didn't want to.
However, MPs also heard from WJEC chief executive Gareth Pierce, who called for "shared standards" in the exams sat across the three countries.
The Welsh exam board WJEC, whose exams are taken by students in England and Wales, is to produce both linear and modular GCSEs.
Yesterday's 'call' on the WJEC to regrade has just been, well, upgraded to a formal direction - in other words, a ministerial demand.
This weekend examiners in Wales are regrading English papers taken under the WJEC examining board, after Welsh Education Minister Leighton Andrews ordered a review of results.
However 2, 400 Welsh pupils have already received better results after the Welsh education minister, Leighton Andrews, ordered the WJEC exam board to regrade Welsh students' papers.
Welsh Education Minister Leighton Andrews ordered the WJEC exam board to re-grade papers, saying the way that grade boundaries were set had been unfair to Welsh pupils.
Following an outcry, Mr Andrews - who regulates exams in Wales - decided to order a regrade of thousands of papers set by the Cardiff-based exam board WJEC.
The WJEC exam board expressed concern at the minister's announcement.
In Wales, ministers ordered a regrade for pupils who got a lower grade than expected with Welsh board WJEC, but Ofqual did not order such a move in England.
BBC: GCSE English: Teachers' anger over generous marking claim
While the talk prompted by the overall figures is that a 100% pass rate might be achievable within a few years, the WJEC has almost reached that point already.
Education Minister Leighton Andrews came under fire this summer when he ordered the WJEC board, which sets most of the GCSEs taken by Welsh pupils, to re-grade English exams.
It will look at possible alternative systems for GCSEs and A levels, including whether there should be one provider instead of allowing schools to choose between competing exam boards such as WJEC.
Mr Andrews said the review had persuaded him the pupils had been the victims of an "injustice" and asked the Welsh exam board WJEC to regrade Welsh pupils' papers.
In 1986 an external examiner for the Welsh Joint Education Committee (WJEC) - the Welsh examinations board - stopped a performance in which a naked pupil simulated a sex act.
Other documents, also released under the Freedom of Information Act, include minutes of a meeting of the awarding committee of the WJEC held after the regrading was ordered in September.
BBC: GCSE English regrade 'damaging', Welsh government warned
He said the "new conditions will ensure that the awarding of the WJEC's GCSE English language qualifications in Wales will be separated from the arrangements for English language in England".
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