I found the issue and now it is about trying to find the solution.
Open wp-includes/js/media-views.js
Line: 8353
_.each( this.$el.serializeArray(), function( pair ) {
data[ pair.name ] = pair.value;
});
This is the js code wordpress is using to collect the form data for submission. It effectively removes the array submitted. I submitted this as a bug on their forums but we will see how they reply.