Sounds like you've got the problem under control already, but as I think someone else mentioned, the problem was probably due to moisture. I've avoided significant problems with flies, and I attribute that to two things: First, I use a droppings board to capture the waste that the birds create...
Starter for game birds has a higher protein content, and that's what you'll want for turkeys, too. Be careful about mixing chickens and turkeys. My understanding is that mixing them is discouraged because turkeys are more susceptible to histomoniasis, or "blackhead." Chickens are...