Get the rust off completely (wire wool or even the plastic equivalent will do), and lightly re-season (thin coat of oil, then cook it on the stovetop--you don't need a "real" seasoning, which will just endanger your interior if it's already good).
Then, don't depend on the seasoning to protect the pan. Always dry it thoroughly before storage (towel dry carefully then give it just a few seconds on the heat to be 100% sure) and make sure the place it's sitting is always dry as well. You might consider placing it on a paper towel or other absorbent surface if you feel that the place you store it can't be kept sufficiently dry, or if you're storing it on a metal surface (to eliminate the chance of galvanic action causing the rust).
If you never leave water in contact with your pan and keep it from being in contact with exposed metal, it won't rust in normal use. A little bit of seasoning on it is a little insurance policy, but as you've seen, it's not sufficient by itself.