It's possible for wild flies to contaminate a culture by laying eggs on the top of the screen. However, I did have a problem with no contamination and fliers developed anyway.
The flies I got that turned into fliers came from a well known frog breeder outside the area. Since the person rectified the situation, I won't say who it was.mindcrash said:Where do you get them from? Is it local?
The only way they are regaining their flight ability is just like everyone said, by mixing flies from two different cultures together. The gene that gives them the ability to fly is recessive, so if you put two recessives together, bingo, you have a flier.
It may be that your supplier isn't aware of this, you might want to inquire.