But overall, the replacement of management allowances by new teaching and learning responsibility points (TLRs) appears to have gone relatively smoothly.
Heads in Wales have until today to agree staffing structures with teachers and governors for the new payments. They then have just under three years to introduce TLRs, while staff on existing allowances have their pay protected for the same period.
Around 34 NASUWT Cymru members at Pontllanfraith secondary, Blackwood, Caerphilly were balloting this week, and the National Union of Teachers Cymru says it has six on-going formal disputes with secondary schools across the country.
NASUWT Cymru says other high-profile disputes - including one on behalf of Monmouthshire primary schools, over advice given to heads about implementing TLRs - have been resolved.
Secretary Geraint Davies said: "There are a handful of schools with outstanding disputes, but most have successfully put in place the new structures. That's a tribute to everyone's efforts."
However, the rival NUT Cymru, which unlike the NASUWT is not a member of the advisory group that proposed TLRs, expects some schools to breach today's deadline.
Secretary Gethin Lewis said: "TLRs have come at the wrong time. A staff review and funding crisis is the worst combination. We are trying to resolve the issues."
Iwan Guy, acting director of the National Association of Head Teachers Cymru, said: "We don't feel this process was necessary. TLRs were expected to cost less than management allowances but that's not going to be the case."