At nearly 1800 hours in the game, and many hours digging through the files and listening to them without playing the game (e.g. while driving), I can't say I recognise what you're saying. I have -all- files coded by name (there is a bank file for that too, you can't miss anything that way), and there are no files left. There were some files that had no sound at all, and I don't know what they were for, but they also don't have any corresponding name in the bank. Aside from that, all files belong to certain civs.
All civs have their own ambient themes, and they start as soon as you settle your first city. There are no general flute themes for all civs. In fact, if you play Maori vs Maori, you won't hear a flute in the game at all. I don't remember flutes in Brazil, Spain, Australia, Zulu, Cree, either, and that's just from the top of my head, so there could be more.
So yeah, if you play a game with Maori, Brazil, America, Greece, Spain, Australia, Zulu and Cree, you won't hear a flute. Especially not at the beginning.
France has a flute from the start, so does Khmer, Nubia, Egypt, Norway and probably a couple of others.