If I understand you correctly I had this happen once. The tube might be getting a little twisted as you install the tire. Once you inflate the tube to be sure it works, deflate it so there is just enough air to "hold its shape." Then install the tire, starting at the valve, and working simultaneously down both sides. Once the tire bead is on, and before you inflate the tire, inspect the tire all the way around, and on both sides, to be sure the tube is fully seated inside the tire, and the valve stem is still in the right place. Then you can reinstall the wheel on the bike, and inflate the tire.

There are lots of videos online that will show you how to do this.