I already solved this so I am creating this for the record.
We were using plain HTML to import CSS and JS, that is not how things should work in Wordpress. Instead you are supposed to use the PHP API to register CSS and JS and use dependencies and what not so that Wordpress can figure out the right order.
In header.php you then use wp_head() which does "the right thing". That "right thing" includes changing the top position to avoid overlap when user is logged in.
I have changed the wpbootstrap_openscap theme to use wp_head and remove the old style CSS and JS imports.
I already solved this so I am creating this for the record.
We were using plain HTML to import CSS and JS, that is not how things should work in Wordpress. Instead you are supposed to use the PHP API to register CSS and JS and use dependencies and what not so that Wordpress can figure out the right order.
In header.php you then use
wp_head()which does "the right thing". That "right thing" includes changing the top position to avoid overlap when user is logged in.I have changed the wpbootstrap_openscap theme to use wp_head and remove the old style CSS and JS imports.