Genghis hit it on the head with this statement:
Where it really goes wrong is where the project management system doesn't allow close liaison with the design team
If that's not set up properly then personality and ego clashes inevitably follow.
From the engineering side we note the old joke about fighter pilots' ego - enhanced at test pilot school from what I've seen in a number of cases.
The last major military project I was involved in had the flight test and project management at loggerheads well before the prototype got on its wheels (which was when the project was cancelled).
I've had more success with smaller civil programmes and worked with a number of well known (and lesser known) TP's in the UK and USA - all marvellous to work with - they understood what it was to work in a team. In Australia, I've experienced mixed success - had a lot to do with the trust that the test crew held in the engineering group at the time. If I start on the Nomad project this could be a long story but some useful lessons amongst it.