One of our journals has a problem with the section order. Although they have changed the order of the individual sections under Settings > Journal > Sections, it does not make an impact in the issue they are going to publish. Could it be that they have now reached a total of 58 section designations. Is there an upper limit?
When I make changes to the section order in other of our journals, it works out fine.
What version of OJS is the journal running on?
This post outlines a similar issue encountered by a user: [OJS 3.2.0-3] Section ordering glitch, please help - #2 by UBWolf - not sure if that’s the issue that you are encountering exactly, but it may be worth taking a look.
Additionally, if you are running 3.1, there has been a reported issue on this, related to QuickSubmit plugin (which has been addressed). This is outlined here: Order sections in issue ojs 184.108.40.206 - #7 by lucaslmdr