I am sure this is user error but I cannot work out what I have done wrong. I have been working on a compile format for my thesis and found that the margins are different for different sections.
Compile
Help gratefully received
Would you say the left indent (not margin per se, as its impossible for the actual document margin to change from one section to the next in Scrivener), increases depending on how nested an item is in the binder? If so, edit your “Thesis” format, and check the Transformations tab for a setting called, Add indent per outline level. If that is checked, disable it and you should be fine.
This setting is nice for making indented outline documents, but probably not much else. 
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Thank you. That was really easy.