My assumption that it's a Bootstrap v3 in Bootstrap theme issue is based upon the original sentence "It works just fine in other themes (except Elegance which is based on Bootstrap) so think it must a Bootstrap issue." with the key object being 'Elegance' and then later discovery that Shoehorn is not being used. As there have been no other indications of unknown Bootstrap v3 themes apart from the known Bas Bootstrap, Elegance and Shoehorn. Therefore a 'Bootstrap v3' applied in a theme issue. So, more logic than assumption.
Themes
Bootstrap and Moodle 2.9
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