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When you add chemistry into a paragraph the Add-In protects its contents by locking the Content Control which is inserted.
A bug exists in Microsoft Word (present in versions 2010, 2013 & 2016) which prevents adujsting of a paragrah’s formattting (such as centering etc) when the first “character” is a locked Content Control. This also applies to table cells and has been reported to the Miscosoft Office Team.
To get around this add a space before inserting a Chemistry object.