Do you find that your allergies are worse in the late fall, after the leaves are down and when it rains a lot?
You may be experiencing mold allergy symptoms. Not only is the outside air full of mold spores and mycotoxins from rotting leaves, but humidity, and therefore mold, can be more of a problem inside as well. Rainy weather often corresponds to increased damp in the basement. This breads more mold. Also, the windows are typically closed against the cold outside, but the furnace does not come on that often, so it can tend towards being a bit cool and damp inside, especially in the basement where many household mold problems originate.
Manually operating the furnace a few times a day to heat and dry the air may help. I find that turning on an electric heater in one room helps quite a bit also. HEPA filters are often effective in reducing the spore count, but do little for mycotoxins.
If you can possibly arrange to have a holiday in warmer dryer climates, November would be the time to do it!