Presta valve inner tube issue: area around the valve does not fill up
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.