I have cracked the issue! Might also be useful for someone else in the future:
When adding an element in a Column, within the Page Builder, for the Special Title it will give you a field and then the text area below. If you enter both Title and Content into the text box, it will strangely start duplicating the ID called sub-title, which is the problem.
So, to fix this, delete the element inside the Column, then re-add it but make sure you enter the Title in the field given, then the Content in the text area below.
Seems to be behaving itself now... I think the Shortcodes.php is set up so when it detects a H tag, it automatically assigns a Div.