I am currently using Build 248.
Say I have a frame with two layers. layer 1 is invisible start of frame. In layer 1 there are backdrop A, B and active object C, D.
When I make layer 1 visible, backdrop B and active object D is not visible (the backdrop will flash in quickly and will be gone). I delete backdrop B and backdrop A is missing.
This is just a simplified scenario of the bug I have. It looks like the only way to fix this is if I remove a fade in transition (fade). The fade in is extremely important in this game and I prefer not to remove it.