Almost 1,600 pupils at Noel-Baker community school in Derby were sent home twice this week in strikes by unions over the same issue.
On Tuesday NASUWT members walked out in protest at changes to senior staff pay, followed two days later by National Union of Teachers' colleagues.
Tuesday's strike was the first in the country by the NASUWT in protest at plans to replace management allowances with teaching and learning responsibility payments and comes despite their national support for the reforms.
Action planned by the NASUWT before Christmas was postponed in the hope that a deal could be made.
Forty-two teachers at Noel-Baker get management allowances. The school proposed to cut this to just 26. Some staff could lose up to pound;8,000-a-year, although salaries will be protected until 2008.
The school also plans to introduce five advanced skills teacher and three excellent teacher posts and employ non-teaching staff for head of year pastoral duties.
The NASUWT dropped the threat of further action, including a two-day stoppage planned for next week, after the school offered an additional TLR and promised to review the changes in 2008.
Paul Davies, Noel-Baker's headteacher, said the school would spend more on staff salaries as a result of the changes.
Dr Davies said: "I am perplexed by what is happening with the NASUWT and unclear what their grounds for dispute were. They are members of the rewards and incentives group and we followed RIG guidance to the letter."
Jerry Bartlett, NASUWT deputy general secretary, said the union was forced to strike because of legal time limits on the validity of industrial action ballots.
He said "A have a great deal of sympathy for the head. He had followed the RIG guidance. There were difficulties associated with his interpretation of that guidance that we have now resolved.
"There would not have been a strike had it not been for the anti-trade union legislation introduced by the Conservatives and retained by this government."
A second school, Derby Moor, will discover today whether NASUWT members have voted to take action.
Under the national deal agreed between the Government, NASUWT and other unions, teachers cannot receive TLRs for administrative tasks. In addition, many pastoral posts are being transferred to non-teaching staff.
Individual teachers will lose management allowances of up to pound;10,500 through moves to focus senior teachers' efforts on teaching and learning.
Others will gain as money is switched towards classroom tasks.
Those signed up to the deal include the Association of Teachers and Lecturers and the Association of School and College Leaders, but not the NUT or National Association of Head Teachers.
The NUT has so far held strikes at nine schools with members at four others due to strike next week. In total, 31 have formally voted for action although some of these have been resolved without strikes. Teachers at about 250 schools have indicated support for action through informal votes.
John Dixon, NUT assistant secretary, said: "We welcome the fact that others are concerned that teachers are losing out as a result of these changes."