Like stated above, most likely under the caulking. I build/remodel/design kitchens and bathrooms for a living, and have been dealing with calls about this in peoples homes for many, many years. Do it right the first time, or you will be doing it again. Remove all caulking in the entire shower, scrub the seams best you can with a toothbrush or something similar, not too abrasive, treat the area heavily with mold treatment (Home Depot or Lowes) or bleach/water, scrub while wet, clean up best you can, spray again and let dry, this is the secret.... must be completely dry! Run fans over night if you have to. Then you can re-caulk. This will hopefully keep it looking good for many years!