I think the problem was coming from not properly registering the scenery.
No, that surely wasn't the problem. If you don't register the scenery, or your activation gets lost for any reason, the scenery will not disappear, but it will revert to Trial mode, meaning all buildings will be displayed, but only for 5-6 minutes at time, and a message will indicate that Trial mode is in effect, when you enter the scenery.
The disappearance of buildings doesn't have anything to do with activation, it's simply an indication the software is not running, for any reason.
What fixed it was probably that, while re-trying, you rebooted Windows, which can help in case FSX wasn't closed properly.