Currently I have a three minute animation with 10 layers, each ordered in a certain way. Why does the layer order change when I click play? i.e. the background comes to the foreground.
I would need to see the project or have more information to know what the real problem is but you can try the following.
-Make sure you are working in the Camera View
-The currently selected level might be showing above everything else, especially if a drawing tool is active.
-There might be a keyframe moving the background in front of everything.