By Tom Symonds
Transport correspondent, BBC News
Network Rail took over stewardship of Britain's railways from the discredited Railtrack and had, until recently, appeared to be running a steady ship, focusing on the day job of slowly improving punctuality.
Network Rail is trying to reduce the number of agency staff it uses
The New Year, with its disastrously over-running engineering work, ended all that, and left the company facing recriminations both inside and outside the rail industry.
The main failing on the vital stretch of the West Coast Mainline at Rugby was a lack of staff to cope with extra work that cropped up during the installation of new track and overhead power lines.
But the report suggests this was symptomatic of a wider problem within Network Rail - the desire to micro-manage from the company's headquarters at Euston station, dubbed The Black Tower by wags in the rail industry.
It meant that when things went wrong on the ground at Rugby, the head didn't know what the hands were doing. Senior Network Rail sources also say there was a desire to push ahead too fast with the work, to be too ambitious.
After all, in any building project, once the wallpaper is stripped off the wall, the true extent of the work required can become apparent.
The same applies to Britain's ageing railway infrastructure. Extra time needs to be built into the plan to allow for the unexpected.
The problem of managing at arm's length is compounded by the continued use of contractors to plan and complete renewals work, involving the rebuilding of sections of line.
For example, Network Rail was relying on outside companies to supply specialised overhead power engineers.
20,000 miles of track
1,000 signal boxes
40,000 bridges and tunnels
Operates 18 major stations
Carries 3m passengers per day
Realising this is a problem, the company is now creating an in-house team of powerline workers, and trying to reduce the number of agency staff it employs.
It has also announced it is setting up what are being called military-style command posts to manage big projects on the ground, where Network Rail and train company managers will make joint decisions to improve the flow of information.
The company has now carried out a review of the progress on the West Coast line and concluded there is a risk it won't meet a deadline of December to finish the work.
The company's chief executive Ian Coucher has revealed to the BBC the work is 315 hours behind schedule, nearly two weeks.
Time for change
To catch up, the section of the line through Rugby will have to be closed for an additional 13 weekends on top of the bank holidays and Easter period during which work is scheduled.
Network Rail insists it didn't need a whopping fine to realise things had to change.
Indeed the penalty has proved controversial in itself.
Politicians, unions and passengers groups have lined up to question the need for the government to fine what is, in effect, a government-funded company.
Network Rail is now making representations to the Office of Rail Regulation to request the money is pumped directly back into the railways. If not there's a worry passengers may suffer twice over.