I assume your spare N9 behaves correctly.

If the problem one miss behaves even after a re-flash and after Nokia have changed the screen (ie: tried to repair it). Then I think you are entitled to a replacement phone, as it's not fit for the job it was designed for.

I don't know where you are from, but here in the UK that is the law, push them to replace it. After all you paid out good money for it, they have seen how it behaves, they have tried to repair it and it still does not work correctly. It's a lemon they need to replace it.