There are a lot of people in the hobby who are confused as to what flies they are selling. There are at least 3 normal mutant strains of flies that are used in these hobbies that don't fly: 1) "true" wingless, 2) vestigial winged, and 3) "dumpy winged" or "flightless" fruit flies.
The "true" wingless have just a nub where the wings should be that is very difficult to see. The vestigial winged flies have tiny, shriveled wings, and the dumpy or "flightless" have wings that are somewhat normal looking, but about 1/3 the size of the wild-winged counterparts.
There is always the chance of spontaneous mutation back to the wild-winged, but it is unlikely. If your flies still can't fly, check to see if maybe you weren't sold flightless fruit flies as wingless. This is a common mistake.
In my experience, the flightless or "dumpy winged" melanogasters are far more prolific than the wingless. Maybe someone else has had different results, but I have heard this from other people as well.
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Homer W. Faucett III, esq.
Purveyor of Trivialities and Fine Nonsense