Confusion is mounting over university admission policies for competitive subjects like medicine and law.
Contradictory messages have been sent out by universities on what happens to bright pupils who sit Standard grades in S3, rather than S4, giving them a two-year run at their Highers in fifth year.
One school in central Scotland was forced this month to reverse its decision to enter some of its most capable pupils for Standard grades in S3, because of fears they could be penalised if they applied for one of the most competitive university courses.
The decision by Frank Lennon, the headteacher of Dunblane High, is the latest manifestation of the unresolved struggle on the part of secondary schools to persuade universities' admissions officers to give equal treatment to pupils who sit Highers over more than one sitting and pupils who have two years to prepare for them.
A number of parents at Dunblane High, which has a strong academic record, have raised concerns that their children could be disadvantaged if applying to sought-after courses with two-year Highers, rather than one.
In one case, the father of an S3 pupil raised the issue with the admissions office for Edinburgh University's law faculty.
He was told: "Highers taken over two years will be given less credit than those taken in the traditional one year format."
Earlier this week, however, following enquiries by TESS, it emerged that this advice was wrong.
"The university takes no account of the length of time an applicant spends studying towards an individual school qualification," said an Edinburgh University spokeswoman.
"For example, if a student takes two years to complete a Higher English course, their result will be valued in the same way as a student who completed the course in one year."
Aberdeen University's admissions service took the same position. But enquiries by TESS to Glasgow, Strathclyde and St Andrews universities revealed that in cases of high competition for scarce places, preference would be given to applicants who completed their Highers over a shorter period of time.
Although reluctant to discriminate against those with two-year Highers, the message was that if push came to shove, this was a criterion they would use in selection.
All the universities stressed the importance of applicants gaining the required four or five Highers in a single sitting.
Head Frank Lennon said: "If there is an admissions policy in operation that schools are unaware of, something needs to be done urgently about that."
He has written to S3 parents giving them the chance to opt out of early presentation, because he "just didn't trust" the universities.
Ken Cunningham, general secretary of School Leaders Scotland, said that universities were "upping the ante" in terms of qualifications because of the competition for places.
"It is difficult to see this not continuing to be an issue, unless universities change their tune - that someone taking a Higher in one year has got a facility that would help them through a degree course. They are using that as a marker, as well as the number of Highers gained over the year," he said.
Larry Flanagan, education convener of the EIS, said the issue had been raised at the Curriculum for Excellence management board but had not been resolved.
A spokeswoman for the Scottish Government said it firmly believed flexibility within the curriculum was an advantage as opposed to a disadvantage.
"The flexibility to study for Highers over two years is a feature of the current system and will continue to be an option under Curriculum for Excellence," she said. "We continue to engage with universities on a range of issues relating to Curriculum for Excellence and the new qualifications, including this matter."