Mutations may occur rather quickly. The expression of those changes wouldn't be seen until the next generation. And speciation may never happen in a way for anyone to see it. It is very likely that it will never be observed at the moment of change. Since that would have to be established and on continuum, where would that be?Things like colour mutations can happen suddenly but I doubt strongly that a new species can evolve over a couple of generations.
Your fly experiment would only be meaningful if you bred the flies in a closed environment. If you're just talking about stray flies entering your house it doesn't mean a thing. Did you keep a record of temperature? I'm not an entomologist (I do know one) but I believe flies have different behaviour at different temperatures.
That is a very good point. Insects are very temperature driven. I used to determine dates of hatch for batches of insect eggs based on the temperatures they were kept at during incubation. Higher temperatures and the eggs mature more rapidly. Lower temperatures and they slow down. It's not sudden, it does take time. But it isn't that long either for many species. Some can remain eggs for an entire season at the right temperature.