The entire are must be completely dry. Sometimes it helps to use a hair dryer and a 24hour fan treatment to ensure this. Also, it is not unheard of to get a bad batch of caulk which does not cure.
Lastly, we would like to see a picture or diagram of this install, because there are no situations where caulk should be the primary waterproof boundary. Do you have a flange on the floor, and overlap the walls over the flange?