It is probably under the paint. We have the same problem in our bathroom - our landlord clearly didn't prime the walls prior to painting them, so about 3 weeks after we moved in, we started getting it on the ceilings and walls above the shower.
If it isn't under the paint but is under the caulking - the onlything you can do it to pull the old caulk out, clean it reall well - paint the gap with and antifungal primer and re-caulk.
Otherwise you are just going to keep having to scrub it, and it will keep growing. Evil stuff that mold.