March 2003 marked a nadir in the relations between the research councils and their academic communities. For the first time in living memory, MPs openly accused one of the research councils of mismanaging its finances.
According to the Commons Science and Technology Select Committee, the Medical Research Council had squandered millions of pounds on large speculative projects, forcing it to reject top-rated applications from leading researchers.
Since those dark days, the council has worked hard to re-establish trust with its community. A new chief executive ushered in a refreshingly open approach. Science-led project grants were introduced to meet the demands of researchers themselves. Support for young researchers was bolstered. And most important, budgets have increased. Morale among researchers has been on the rise.
Yet all this hard work threatens to be undone after the revelations this week that the MRC - and other research councils - once again appear to have messed up their finances.
This time officials have underspent rather than overspent. The MRC managed to underspend by some £52 million - a tenth of its total budget - in the past academic year. Council sources report that the total deficit for all the research councils is several times larger.
All this comes at a time when success rates for research applications are alarmingly low: some councils give awards to only 15 per cent of applicants.
Whatever reassurances the councils give, researchers across the country will jump to the conclusion that top-rated research proposals will have been unnecessarily turned away and basic science will have suffered.
No one underestimates the challenge of overseeing annual budgets that can now total half a billion pounds, comprising thousands of grants running over different time scales. (A recurring problem for the councils is the millions of pounds of unspent money returned by universities.) But academics will point to two inescapable facts. First, the sheer scale of the underspend. Second, evidence that some research councils have dealt with the problem better than others. Surely an accounting system can be devised that avoids such major oversights.
On the plus side, the MRC has been open and candid about the issue. Its fellow councils were less willing to put their heads above the parapet.
Perhaps the most damning criticism of the MRC by MPs two and half years ago was that it had kept the community in the dark about its financial problems - blighting the community's ability to plan ahead. The challenge now for the MRC is to maintain that openness, attend to its accounts and reassure researchers so that morale is not harmed for good.