C.M.
My daughter (almost 20 months) did the saem thing. She would drink milk all day long (if we let her) out of a bottle but didn't want it in a sippy cup. She just now started drinking some milk out of a sippy cup (after about 1 - 1 1/2 months). I mix a little choc. milk in and she seems to like it now. She LOVES her cheese so we don't worry as much about it anymore. So been there, still working on it, but she soon started to realize the "ba ba" was gone and all she was getting was the "sippy"!
So I agree with some other moms, don't worry too much just offer other forms of calcium and don't give up just yet on the drinking milk thing. Hopefully soon, he'll come around! Good Luck!