Junior Cycle students are facing the prospect of a two-tier exam system as schools reopen without any resolution of the row over reforms.
And the union blocking the changes, the Association of Secondary Teachers Ireland (ASTI) is now at the centre of an embarrassing internal dispute.
The first of new-style assessments for pupils is due to be rolled out in May - but, while one in three schools is ready, teachers elsewhere are still not co-operating.
Meanwhile in the ASTI, about 20 staff - that is, most of its employees - are taking the union to the Workplace Relations Commission over an industrial relations matter.
The staff, members of Siptu and the National Union of Journalists (NUJ), are unhappy that union leadership has not defended them against criticisms made in the media and on websites by a small cohort of ASTI members.
An ASTI spokesperson declined to comment on the matter.
It is not the first time that strains have emerged within the ASTI.
At the union's 2014 conference, then general secretary Pat King, who retired recently, condemned death threats to him posted on a Facebook page run by a group calling itself ASTI Fightback. The group denied knowledge of a death threat and said any personalised attacks would be removed.
But last September, the union demanded the group desist from using the ASTI name in its literature - and condemned comments made online and in print which it said undermined the integrity of staff.
More than a decade ago, the Labour Court told the union "to get its house in order", declaring that its head office staff were working within an environment of fear, where threats were common.
The latest internal difficulties come as the ASTI continues its stand-off with Education Minister Jan O'Sullivan (below) over the Junior Cert.
Despite ongoing ASTI resistance, Ms O'Sullivan decided to press ahead with the reform process in the hope that agreement would be reached with the 18,000-member union - but no progress has been made.
Teachers' Union of Ireland (TUI) members accepted the changes and are being trained in how to equip students with modern-day skills.
The first of the new assessments for current second years is due in English this May.
The teachers undergoing training work in about 250 of around 730 second-level schools - those in the education and training board sector, where the TUI represents teachers. A key aim of the reforms is to end the reliance on a set of terminal exams at the end of three years in junior cycle - which encourages rote learning - and replace it with a dual approach to assessment.
Under the new system, students would also have two classroom-based assessments - one in second year and one in third year - such as oral presentations and projects.
The idea is to develop a range of important skills, such as oral communications and a spirit of inquiry, while a broader assessment model will provide a more rounded picture of a student's abilities.
It means some pupils will be exposed to the most modern teaching and assessment methods, while others will not.
ASTI is the sole union representing members in about half of second-level schools.
There are more than 90 community and comprehensive schools where both unions are represented. A decision will be taken soon on whether TUI members in those schools should also be invited to train.