Hi, Brian. If there’s a theme conflict, the issue could be anywhere, but I’d recommend looking through the theme’s code for anything that filters $wp_query — it could be that it’s intending to affect queries but isn’t limiting itself to not affect queries that aren’t its own.
Since we don’t provide support for themes other than the WordPress default themes (e.g. Twenty Fourteen, like you tested), you’ll need to contact your theme author for support on this issue if you’re unable to figure it out on your own.
Please let me know how this goes for you.