I have been experiencing allergy-like symptoms after aerobic type exercises such as runnign or bicycling. After a moderate workout, I can experience snezzing, runny nose, tearing eyes, congestion. This can happen right away or has taken a full 24 hours to present symptoms. I would say it happens about 40% of the time after I run. The symptoms are so severe that I can't do much but rest. Usually unable to go to work. The symptoms can last for 12 hours or up to 3-4 days. The symptoms are usually unilateral on my right side, have also been on my left side (5%) or bilateral (5%). I have tried MANY allergy medications, Singulair and the like, eye drops, nasal sprays, OTC allergy medicaitons. None have worked. I have exercise induced asthma for which I take albuterol. I have hypothyroidism for which I take Synthroid. I have seen an ENT-negative. CT sinuses negative. I have seen a Naturopathic doctor who thought it might be a lacrimal duct spasm causing non-allergic rhinitis.
I would definitely go back to your naturopathic doctor and ask him to analyse if you have fungal overgrowth. If this is the case, then this dysbiosis may be particularly apparent on any membrane surfaces, which will increase their permeability whenever you exercise/sweat. Do you have any 'brain fog'/carb cravings/itches/tiredness?