As Chris_b says, I'd not worry about any long-term effects, it's most likely your ears haven't equalised the pressure yet. For me it can take three or four days for things to go back to normal after a bad flight. If it persists, do go to the doctors - the movement of the wax and fluids caused by the pressure changes can trigger an infection (it did me a few years ago).
If you find you suffer from this a lot, try taking decongestants for a week or so before flying, it helps me a great deal.