Leather's salary was increased from £50,000 to £75,000 in 2007/08 in order to recognise the extra hours she was working, the commission said.
Leather started with the commission on 1 August 2006 on a salary of £50,000 for a two-day week. But her contract was changed the following year because she was working much more than that, according to the commission.
The change to Leather's salary was agreed by the Cabinet Office and the Civil Service Commissioners in 2007 and details were published in the commission's accounts in July this year.
Leather now has a salary of between £75,000 and £80,000 for a three-day week. The backdated pay amounted to £14,402.
A commission spokeswoman said: "The increase from two to three days was a routine amendment to Suzi's contract. As far as we can see it wasn't communicated at the time to all staff because there was no need. Staff saw Suzi working three or four days a week, and nothing there changed.
"You may also be interested to know that Suzi often does visits to charities on her own time."