First guess would be bacterial vaginosis, since a bad smell is one of its hallmark symptoms. You said "internal swabs came up negative," were they testing for BV?
Did you have a standard pelvic exam, with a speculum and the doctor looking up inside your vagina? Second guess would be a forgotten tampon, but it would have to be a poor job if a medical person did a pelvic exam and actually looked and didn't see an old tampon.
Have you had any odd periods or a recent miscarriage? Sometimes a little bit of tissue can linger in the uterus, but I haven't heard those are related so much to a bad smell.