Since this thread got very long, I want to clarify some things (since the Dropbox link is dead).
You have maps in the Maps to always cook list, right? If you clear and reset that list, then everything is fine?
We have a fix for this, where the paths are stored like /Game/Maps/… but it is coming in a little hot for 4.11. It sounds like you have a workaround (reset the list), is this correct?
Josh