I have the same thing happening to me on version 5.3.1
The problem
When having a WYSIWYG field under a tab in a Flexible Content layout, the output of the_sub_field() stripped the content of its tags. Shortcodes did not work either.
The solution
Moving the WYSIWYG field to the top of the Flexible Content (meaning not under a tab field). This worked for me and it formats shortcodes and tags again.
I could also place the field back under the tab now, and it worked just fine.
