I'm the author of the Graphene theme, and unfortunately the fix you suggested can't be implemented, as it'll remove the functionality of filtering the home page posts by category.
I did quite a bit of digging, and found out that the bug actually lies in the Meteor Slides plugin itself, and not the theme. This is because the plugin creates a new query within the WordPress main query to display the slides within a post/page, but didn't destroy that query data properly after using it.
The file where this bug is located is
meteor-slides/includes/meteor-slideshow.php. The plugin uses the
WP_Query class to get the slides, but resets the query using
wp_reset_query(). It should be using
wp_reset_postdata() instead to clear the custom query data, as
wp_reset_query() is for the
query_posts() function, and not the WP_Query class.