I think you should see a dr. ACs are notorious for harboring molds. You could have a mold allergy and in your case with swelling of the mouth causing breathing issues, whatever is actually causing it is serious. If you can't get to a dr quickly, get some liquid Benadryl to try the next time this happens.
I had some itching with pollen allergies this spring. The liquid gels worked great as a boost to my normal antihistamine for the itching. They were very portable and still and liquid for faster effectiveness.
See a dr.
Have you tried putting a filter in the unit, this will sometime help to trap any impurities, dust mites, pollen, or any other allergen. Having your window open probably makes the a/c air less potent,therefore, you do not notice the problems as much.