My daughter is allergic to cows milk.( I remember telling her pediatrician that she was born congested!) When we got confirmation that she was allergic, my plan of attack was just to cut out direct sources of cows milk/diary in her diet. But she still was congested and getting sinus infections-ugh! So then I started to read the ingredients in all the other food that she was eating (not only looking for milk, but for butter, "casein", "whey", cheese, etc)... and once I cut out that from her diet, her congestion got much much better. So you might want to review the ingredients of everything else that she's eating to ensure there aren't secondary sources of cows milk. (And if you're still breast feeding, you might try cut those items out of your diet also and see if she improves.)
Also, (and I have a feeling that you won't like hearing this... sorry!) I have heard that there is a high incidence of dual allergies among infants/toddlers with cows milk and soy:
"A significant percentage of babies with cow's milk protein allergy will also react to soy..." http://www.kellymom.com/babyconcerns/food-sensitivity.html
One last thought, around 24 months, my daughter's overall congestion and sinus infections improved. We have xray data to show that there was significant maturity development in her sinus cavities between 18 months and 24 months. So, another thought is that you might just have to wait another 6 months for her sinuses to naturally mature.
Good luck.