For me, Zyrtec works better than Allegra, but Allegra-D is a good medicine. Have you thought about adding a nose spray to your routine?

I've been on Allegra-D for a few years and have had some problems recently, too, even when using it and Flonase. My doctor added Singulair as well and that has really helped me so far.
My friend is on Zyrtec and is having some bad allergy problems with it as well, so I think maybe in some parts allergy season is just particularly bad this year.