You haven't actually asked a question, but am I reading it right that you are asking how to resolve differences of opinion in programming delays ?
If so, as a Contractor, it is your programme, so make sure it is a good one, not just in logic, but presentation. Programmes with thousands of activities/operations may be very well thought through, but not easy to understand. Years ago, I read that people struggle to get their minds around programmes with more than 50 or 60 activities, so my tip is to use levels of programmes i.e. the Highest level has not more than 50 operations, with in a an ideal world, each operation breaking down into not more than another 50 activities.
Another one is explain it to the PM in a way that makes sense to them answering queries verbally and making minor adjustments etc as you explain it. More major ones are agreed in principle before the programme is submitted for acceptance.
Likewise, when assessing the impact of what is quite clearly quite a major compensation event, explain it to them before submission and effectively agree it there and then.
Final comment (although I could go on): you submit it to the Project Manager, not the Employer, for acceptance who has a duty to act impartially.