Hi,
The new version is creating sub-menu items for other languages than the current one if you use Show in Menu option. I see your menu system is using different structure for sub-menus, it has additional dropdown class and on hover it adds open class, that does not happen for languages and the dropdown never appears.
If you need to keep the flags in one line, like it was before, then disable Show in Menu configuration option in GTranslate settings page and add [gtranslate] shortcode into the menu directly, so it can render side by side like the old version.
You can go to Appearance -> Menus -> Custom Link then set URL = # and Link Text = [gtranslate] then Add to Menu. Please check Positioning tips for more specific examples.
If you want to have sub-menu items like your other menu options, then please consult your theme/menu developer.
Thanks! ??