Well, what are you using for fruit fly medium? Anything homemade with potato flakes is bound to cause an awful smell. How long are you keeping the cultures around too? Mine start to smell like old fish after a few weeks when it turns blackish brown. By then, I would just discard them. I keep most of the backup cultures in the basement in indirect light. I keep two or three active cultures upstairs in my bedroom in a corner.
If it smells strongly of yeast, you may be adding too much. Also, lots of starchy foods other than potato flakes like flour (added to make the medium more solid) can cause a smell. How much ventilation are you giving the cultures? Not enough circulation is bound to cause lots of moisture buildup and rotting conditions. I learned that the hard way first starting out. Read my article about giving the flies max air circulation with the
Re: Beginner's dart frog advice by "bast"
I posted information in this topic a day ago, since he asked about any dart frogs eating more than fruit flies. I explained how easy they are to culture.