Gordon Brown must feel he can't win on MPs' expenses. His first attempt to clean up the system, pre-empting the review by the Kelly Committee on Standards in Public Life by issuing his own proposals, is remembered only for his infamous YouTube video.

Yesterday, another well-intentioned move – the independent audit of all claims by MPs over four years that Mr Brown announced in May – also boomeranged and left the Prime Minister with the biggest headache so far. He will repay £12,415 after Sir Thomas Legg, the former mandarin conducting the investigation, judged that he claimed too much for cleaning bills.

Although he did not breach the rules that existed at the time, it is a large sum that can only make his battered public image even worse. Mr Brown had hoped the Legg inquiry would complete its work by July but it dragged on.

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The final element of the clean-up would be this month when Sir Christopher Kelly's anti-sleaze committee proposed a new expenses regime for the future, drawing a line under the damaging affair before the general election. Sir Thomas has clearly been more forensic and tougher than ministers bargained for; they expected a few bad apples would be asked to pay back money, with the rest given a clean bill of health.

Now the Legg and Kelly reviews are overlapping, prolonging the agony. Detailed claims by all MPs over the past 18 months will also be published this autumn – without the blanked-out pages which turned the previous instalment covering 2004-08 into a farce.

Not for the first time, a Brown initiative has not gone according to plan. Although David Cameron and Nick Clegg are also implicated in the Legg review, MPs in all parties believe the two main opposition party leaders have been quicker on their feet in the expenses saga than Mr Brown.

Even when he takes decisive action, he gets little credit for it. As the governing party, Labour was always likely to take a bigger hit on expenses than its rivals. It is true that some of the most embarrassing claims (such as for duck houses and moat cleaning) were from Tory MPs. Quick action by Mr Cameron – and some rough justice against old guard MPs – limited some of the damage.

When Mr Brown followed suit and cracked down on individual Labour MPs, it rebounded. The Norwich North MP Ian Gibson resigned when he was deselected as a Labour candidate, provoking a by-election won by the Tories.

Yesterday, the atmosphere in the Commons was tense, as if MPs had been dispatched to a new, unfamiliar school for the new term, and anxiously awaited an instant disciplinary report from draconian Headmaster Legg.

The expenses issue, barely mentioned during the party conference season, now tops the political agenda again, drowning out Mr Brown's attempts to turn Labour's fire on the Tories. Cabinet ministers fear its long shadow will not lift by the general election. And that is bad news for Labour.