I suffered from this for about a year and it did not appear to be related to a cold. The worst case was during my one and only flight in a Jet Provost when we dived from 11000' to low level and I was in agony, couldn't even get to rub it because of the helmet.
My doctor recommended Otrivine (non prescription decongestant) and I never had a problem when I used that immediately before a flight.