A funny and simple bugfinding trick is to start deleting large parts of the events and check if the error is still there. If it's eliminated, delete smaller parts and check again, until you pinned down the event that causes the unwanted behavior.
In this case I do blame linkman! :D
Well, the "Setup following" action of the Magicam object apparently doesn't like it when you load stuff on start of layout, IF you set a lag. 0 lag will be fine.
Apart from simply setting lag to 0, which you probably don't want, you can just push the "Setup following" action back. For example make it an action of event 9 where the condition is "Timer is equal to 4000" and place it right after you set the position for the player ship. Then it will work correctly.
Why it does work when the layout is the first in line, might have to do with things going down differently on software startup.
Other than that let me advice you to point out any custom effects and plugins you're using (or delete them from the project before you upload), because users interested in helping you might not bother to search the forum for the needed items.
Good luck with that game (and please do discover the function object *hint*)!