Same problem here with the loose flies and not being waterproof. I have been looking at the MFC River Camo foam fly boxes. You can add the swing leaf that adds capacity for close to 400 flies. Some friends like it enough to buy more of themI have been using the Tacky box this past year. The problem I have with it is it seems like every time I open it, I have a loose fly. I have re-checked every fly to ensure they are securely in the slots, but it continues to happen. They are also not waterproof.
It funny you posted this, I just ordered some tins and foam from amazon to do the same thing. I just wanted some cheap boxes I could fit in my jeans pocket to hold a handful of flies. I found some foam sheets with adhesive backing, if it works, I'll post the materials here.