I think I'm developing a fruit fly allergy.
1.) What are the symptoms?
2.) Are you raising them on purpose, or do you just have an infestation?
I raise them for my amphibians, and I get a scratchy throat when I'm in the same room as them. I have them in my bedroom, where I spend most of my time, since it's the only place that's both warm enough (can't put them in the garage or loft) and that won't bother mum with the smell they produce. I'm thinking of making an insulated heated enclosure for them that I can put in the garage.
Is it possible that you are allergic to their excrement and/or dust? Maybe you could find teeny-tiny diapers for them.
Yeah, it'll be the excrement and/or dust; probably lots of tiny fly hairs and poop particles wafting from the cultures to my lungs. Some people develop an allergy to crickets from raising them as food for reptiles; it's a well known hazard. I just finished making an insulated enclosure in the garage; I turned a shelf into a compartment with 5cm thick polystyrene all around it, and put a couple of large air pumps in it. The pumps supply air to my tanks in the garden, and they produce a fair bit of waste heat (they can become too hot to touch in warm weather, and their cases are big metal heat sinks). Hopefully the flies will be toasty-warm in there, and my throat will stop feeling like I inhaled a Brillo pad.