It seems like a similar issue I had a few months back after a flash. I'm not sure what could have triggered it, but, definitely one AP wouldn't work at all which was fine with other phones (even another N9). I didn't mind it back then as that was not the default connection I use to connect to internet. After a recent flash, when I tried with the same AP, that was totally fine the problem was rectified.

Would a 'restore settings'help? Not sure.