Cubic theme//site logo image not appearing.

Looks like your shortcodes plugins is redefining the generic class clear – which is already used in Cubic. Since your shortcode sets the clear class to be invisible, that’s why it’s hiding your branding area, including logo and site title.

I suggest you deactivate your shortcodes plugin to confirm that’s the culprit. Plugins should always namespace their classes by prefacing them with a unique prefix (like utsc_clear) to avoid conflicts like this.