This one is a bit weird and although I'm now testing it with version 1.43, it has started a while ago when I first switched to Unity5/AC1.42. The problem is that the order of image effects on the main camera is reversed (I think) after quitting and restarting Unity (or after switching to another scene and coming back).
I created a new project, imported AC1.43 and imported the Image Effects from the Standard Assets. I then created a scene, pressed "Organise room objects" and loaded a few arbitrary image effects onto the main camera. I saved the scene and quit Unity. When I re-opened the scene, the order of image effects was not the same as the one I have previously set. Just for the sake of testing, I also added an additional Unity camera to the same scene and placed the same image effects, which I have previously placed on AC's main camera, onto it as well. This camera did keep the image effect order after quitting intact while AC's main camera did not.
Please feel free to request any further info.
Thanks.
Comments
I don't know of the best way to counter this, save for remaking the MainCamera local to the scene, and deleting the prefabbed one stops the issue occuring. It's possible to break the connection automatically through script when the Scene Manager creates it, but I'm too comfortable with that.
That'll at least tide things over until a proper fix is issued.