I have same issue, after updating all flags gone accept english flag, i have delete the plugin and installed again but it seems the issue still available.
Hi,
I think it is similar to this one: https://projectdmc.org/support/topic/remove-flag-of-the-current-language/
You can use [gtranslate] shortcode instead of Show in Menu or you can create individual menu items with [gt-link …] shortcode, please refer to Positioning tips in GTranslate settings page.
Thanks! 🙂