I have this problem I keep running into and it's getting pretty expensive. I've bought many inner tubes and when I pump the tire up with air, the inner tube fills up really good except in the area where the valve is. That area is still completely flat and I can't figure out why. I use a Presta valve adapter since I use a mini hand pump that doesn't have the Presta pump hole...could that be the problem?
When you fill up an inner tube outside of a tire, the area near the valve will look a bit constricted because the rubber is reinforced in that area:
However, when you fill it inside the tire, don't worry - there's enough stretch in it so that it will expand to the right size and work properly.
The same goes for patches. If you fill the patched inner with air outside of a tire, the patches will deform the tube, but it'll still work just fine once in the tire.
The adapter shouldn't have an affect on whether the tire pumps up properly, or not. You might try pumping the tube up, before installing it. The tube could be sticking together at the junction. When the tube is outside the tire it can expand, and hopefully that junction at the stem will expand as well. Of course, you'll need to deflate the tube before installing it.