piggy, my OH suffered severe sinus pain at altitude a few years back (at its worst, made flying - and driving in mountains - very painful. His consultant determined that he had an obstruction/pinch in one of the little tubes from the sinus cavities, so the pressure in his sinuses wasn't adjusting to altitude. It was dealt with under general anaesthetic, and he's fine now.
This doesn't answer your question but it sounds similar to nanny's daughter's problem. Do see a consultant if you can.