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Well this is weird, please give us some more time to look into this issue.
We will try replicating this on our test site.
Thanks for the patience.
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We tested this on our test site and we were unable to replicate this issue.
Please make sure you are not using any cache plugins.
Try clearing your cache.
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English page : http://prntscr.com/fcczi2
ES Language page : http://prntscr.com/fcczmv
The translation seems to be working completely fine.
The issue related to the English flag not showing up in the courses page is related to wpml.
Everthing else related to multilingual seems to be fine on your site.
Please contact their support forums.