Edexcel's GCSE maths pass mark was lowered by eight percentage points this year, an examiner who supervised the change revealed to the Sunday Times.
By contrast, some teachers complain that up to 4,000 students received lower GCSE maths grades because raw marks were rounded downwards this year to bring maths into line with other subjects.
Meanwhile, last week's TES survey suggests that pupils have produced the biggest ever improvement in GCSE results, with more than 54 per cent gaining at least five top grades.
The latest exam-fixing claims are unlikely to rival last year's A-level trauma, but they have already cast suspicion on this year's achievements.
The Tories have predictably demanded an inquiry. But such inquiries rarely get to the heart of the matter. They might stop the allegations for a few months, but they don't prevent them re-emerging the following year.
The then education secretary David Blunkett established the Rose inquiry into key stage 2 test marking in 1999 after newspapers claimed the pass mark had been lowered for political reasons. The Tories and Liberal Democrats nominated members to a team headed by former senior schools inspector Jim Rose.
The inquiry found the allegations were without foundation. Yet newspapers continued to allege the results were fixed - at least until they stopped improving. Now, just as secondaries achieve significantly improved GCSE results, similar charges are made.
But, instead of another inquiry, the Government should ask the Qualifications and Curriculum Authority and the exam boards to introduce greater transparency and simplicity to GCSE, A-level and national test marking.
Three changes are needed. First, the boards and the QCA must cut their remaining secrecy. Confidentiality is obviously vital before pupils sit exam papers. It is not necessary once the papers have been corrected.
But exam boards fear openness. They resisted the right of students to see their marked GCSE and A-level papers, warning that this would create an avalanche of appeals, which never happened. And it took crises for headteachers to be given a monitoring role.
All the marking and grading decisions that examiners make and the reasons for them should be published once they are finalised. While they remain secret, newspapers will continue to uncover great "exam-fixing scandals".
The second problem lies with our obsession with grades. This makes it hard for students who narrowly miss a C or a B. It also makes it difficult for universities to distinguish between those with the top A-level grades.
Students' actual marks should be published and these should also be reflected in the performance tables.
Outside the examiners' world, few understand why pass marks are altered every year. Such grade boundary fixing may be designed to ensure comparability of standards and fairness for students. But its effect is to undermine their achievement.
It is time to stop this statistical magical mystery tour. Pass marks should stay the same from one year to the next. Students should know that 50 per cent will always be a C at GCSE or a level 4 in the key stage 2 tests.
Such change would require better preparation of the exam papers to ensure that the difficulty of questions is maintained, but that effort would be a small price to pay.
Unless the system is opened up, allegations will continue to be made. They will undermine the success of schools that are making genuine improvements and make it harder for education ministers to win more money from the Treasury. Then we could start celebrating success rather than forever decrying it.
Conor Ryan was special adviser to David Blunkett at the Department for Education and Employment, 1997-2001