How did you use tween? What layers are involved in the tweened frames and how are the layer contents being transitioned between frames? In the Frame anination timline you posted which frames were generated by tween?
Okay so I opened the new file then said make frames from layers. Then when I selcted the two layers I want to fade into each other and clicked tween the inbetween layers are coming up as alomost a png like transition which I think is causing the flash.