In my experience, once the costs have started to escalate, the Employer / Project Manager do not want to accept a programme that could be financially embarrassing, they therefore prevaricate over anything until the project is completed when they try and usually succeed, in "doing a deal" with the contractor, who does not want years of adjudications which will cost him money and then possible litigation. This in my experience usually favours the Employer which is what he has been aiming for all along.
The only way to counter act this would seem to be adjudicate early, but where does that leave the " spirit of mutual trust and co-operation". I am often considered to be too aggressive as I try and exercise by full rights and entitlements under the contract; every contract I have worked on where the Contractor has tried to play "Mr. Nice Guy" to the Employer, not used the contract properly to ensure their entitlement and expected the Employer to do the same, has resulted in the contractor losing out.
Ensuring all notices are submitted and that you maximise the potential recovery is the only way to run the contract, if you want to keep in the Employers good books, the contract does not say you have to apply for your full entitlement, but if you havent gone through the right processes you almost certainly will not get it.