The 6am and 6pm stamina bonuses are not part of your stamina bar.

They are part of the muscle icon found under your stamina bar.

At 6am and 6pm of your server's time, that icon shows up, and you begin to consume its 30 stamina instead of your regular stamina.

Only when those 30 are depleted (and the icon is gone), will you begin to use your regular stamina again.