If your girlfriend has bacterial vaginosis or a yeast infrection it can get trapped under your foreskin. There, it can breed and spread, causing the foul odor. When you take a shower, you probably get rid of some of it (which decreases the smell) but it is still there. Switch to antibacterial soap (Like NuSkin or Dial) and see if that helps. If not, see a doctor.
I wouldn't be too worried. If you've already been to the doctor, and both you and your girlfriend have both checked out in good health, there isn't really too much to be concerned about.
CurleyGirl7 has some good advice, if your girlfriend does have a yeast infection or vaginosis, that could very well be causing the smell.
Don't doubt your girlfriend like someone suggested, if this is really concerning you, I doubt your girlfriend would lie about being healthy or not. After all if it was serious, it could be dangerous to her too.
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