1) Not sure how old she is now, but if she is at least 6 months old, consider getting her off any milk based products including formula (soy is not a good alternative as it still contains casein). If you are nursing, cut out all your milk products, if you are on formula, consider going with a almond or rice milk with cod liver oil and a vitamin. Many milk allergies/sensitivities have symptoms of chronic congestion, runny nose.
2) If her mattress is not organic rubber, cover it with a allergy cover from target or gaiam.com or wal-mart. Make sure it zips over the mattress to stop any dust mites, etc.
3)DO NOT VACCINATE her while she has this congestion. Please, please, read on this. Even the pharmacutical inserts suggest delaying until the child is WELL. Well is not congestion that can be heard in the breathing. Also, if she turns out to have food allergies, especially egg, the vaccinnes are made with egg products - you could be injecting her with something she is allergic to and can cause many other problems you don't need. Delaying a few vaccinnes until you get educated is not going to cause any harm.
4) Consider dressing her very warmly and turning the heat off at night. My sisters and I had congestion when we were small and the pediatrician told my mom to turn it off. She did and we were compeltely better. We always just thought they were cheap!! HeeHee.
5) If none of that helps, I would get a IGG food sensitivity test done on her. It is bloodwork. The doctors will say food sensitivities do not matter and I have every child in my family to prove them wrong. If your doctor won't write the lab orders, send me a note and I will give you all the ways you can get it done with insurance coverage.
6) Sorry, I thought of one more. Saline rinses in the nose. We use a neti pot, but when my daughter was too young, we used a medicine dropper. Mix 1 cup warm water with 1/2 tsp sea salt (get a good brand, fine grind). Suck it into the medicine dropper and drip it quickly into her nose. Yes, it will go down her throat, but it will still work. As she gets older you can do the neti way and it won't go down her throat.
HTH - J.