In 2009, after a long-running dispute with the board about his obligations and entitlements, John Nicol and the board entered into a binding record of settlement, the authority said.
John Nicol was owed 70 days of accumulated leave, and under the agreement it was decided that he would take 35 days of annual leave immediately, and receive a payment of $10,100 for the remaining 35 days.
However, John Nicol told the authority that he believed the sum was paid to him as compensation for stress and he was entitled to payments for a further 35 days' annual leave.
The authority found that several errors had been made in terms of John Nicol's pay as a result of the Novopay system.
The board stated that John Nicol was paid a final sum of $15,821 when he should have been paid $4597.
However, John Nicol claimed that he was owed $34,896 by the board.
Steven Nicol's employment ended in September 2012 after he was made redundant, and the board acknowledged that it owed him $2193 in redundancy pay.
However, the board told the authority it was withholding this amount as they believed he had also been overpaid by Novopay.
The board said Steven Nicol was paid the final sum of $5411, when he was only due $403. However, Steven Nicol claimed he was owed the sum of $3953.
Authority member David Appleton found that John Nicol was overpaid and was not entitled to an additional 35 days' leave.
The amount of money he owed would be determined at a later date.
John Nicol was not eligible for other entitlements, Mr Appleton found.
Steven Nicol received an overpayment of $2138, Mr Appleton said. He ordered him to repay a figure yet to be agreed.
Costs were reserved.
Both parties were being sought for comment.
South Otago High School Board of Trustees chairman Brent Gardner said the board was happy with the decision, and felt it was fair and just.
Post Primary Teachers Association general secretary Michael Stevenson said the PPTA put 113 cases before the Employment Relations Authority last year, but all cases were all settled before a hearing was needed.