Assuming this is a theoretical scenario?
My thoughs are:
The microwave only has sufficient leakage to earth to trip the RCD when it starts to cook so it doesn't show when PAT tested.
The offending socket is nearest to the consumer unit, so it has a lower Zs than the others.
The leakage of the microwave is only just over the operating current of the RCD. Therefore it operates when plugged into the nearest socket as the Zs is low, but the slightly higher Zs at the other sockets is enough to prevent the RCD operating.
I'm not convinced by my answer, as I suspect the fault on the upstair lights is connected, despite it seemingly having been rectified.
As I say, I'm taking this as a theoretical question to test us, rather than a real situation, so I'm assuming you've given us enough details to solve the problem...