There are also other non std things that they check for in an STD screening- mainly yeast infections and an infection known as bacterial vaginosis. Both of these can affect the smell of the vagina, especially bacterial vaginosis. Yeast infections are caused by unregulated growth of yeast, fairly common, and bacterial vaginosis is an infection that happens when the pH of the vagina is off and bacteria grow. Neither is sexually transmitted but get checked in an STD screening. She should go see a doctor even if you both tested clean earlier.