1. Could you be having seasonal allergies (it's that time of year) or a cold (lots going around)?
2. Have you tried adjusting the humidifier? Some people have more congestion if the humidifier is too high, other's have it if the humidifier is too low. Mine has to be just right (like Goldilocks!). I have sinus issues if I turn it up OR down.
It seems to be more common to have issues if the humdifier is too high, so if your humidifier is on a middle setting, try slowly lowering it--perhaps one notch every 3 to 5 days and see if you feel any better or worse. If worse, turn it up slowly.
Some people are really sensitive to the humidifier and either run their humidifier in passover mode (I used to think it was for Jewish people
but it means having the humdifier attached but no heat at all) or take the humidifier off completely.