POBJOY.
It seems as though the flying side was watertight and that those that ran the organisation were doing a good job. After all, the transition to MAA regs etc appears to have been straightforward.
The issue with engineering seems to have set in following contractorisation when the engineering was taken out of the hands of those who run the organisation. They say that "a camel is a horse designed by a committee" in other words complex organisations can get things wrong. I am not sure how many moving parts there are in the engineering organisation but as a starter for 10, I reckon: the MAA, the RAF, the contractor, the PT, HQ ACO and the design organisations. All of these can drop the ball but with so many it is difficult to tell when and where it has been dropped. I wouldn't mind betting that part of the recovery solution has been to chuck even more engineers and organisations at the problem - each with their own agendas. Just because there are so many engineers attacking the problem I looked up on Google the collective noun for a bunch of engineers - it came up with an "Awkward of Engineers".
I feel for them actually. Having declared the aircraft as not airworthy they're going to have to make damn sure that they are, and they can prove it, before they put them back in the sky.