Why does this happen?

As you can see in the first pic in C2 I have everything set up and aligned in the right positions, but when I try to run the layout in the broswer everything is misplaced.

Why does this happen, how can I fix it?

If you can upload a CapX we can look at it for you. It may have something to do with your scaling settings or parallax settings though. Are you setting the position of the objects in events during runtime or scaling the objects themselves?

Maybe you need to check this :

Yeah, it looks like setting parallax in editor to yes shows me that they are screwed up in C2 too. I'll try to rearrange them, thank you.

Sorry Xerullian, but I'm beyond the point where I feel comfortable uploading a capx. As for my settings I use scale outer and parallax is set to 50/50 for the sky layer and 100/100 for the other layers.

Understandable not wanting to upload a capx. What I might suggest doing then is trying to reproduce the error in a separate capx that doesn't include your whole project. I usually find when I separate the parts I can see where the issues are popping up.

That way if you want to post something for more help you don't have to show off your whole project either.

Indeed it's something to keep in mind. Thanks mate.