Ya, if you check the store and they don't have the color you want, you need to back out of that pop-up window, select a new color then check again. It's annoying but helps.
Also you might want to call your store to make sure. I wanted the white but my local store showed they were sold out. I decided with the black then since they only had two left. I went to the store, told them I wanted the black since the white was not available. The guy came back from the back with a white and said it was the last one they had. So the check store status is NOT always correct.