Will it not seal on the stem?
I used to try to press my pump fitting down all the way because I thought that the fitting had to press in the valve stem. I have found that the fitting doesn't have to press the doohickey down to allow the tire to take air.
I always bleed a bit of air out of the tire before putting the fitting on. This creates enough of a pressure difference for me to be sure that air is transferring to the tire. When I build pressure in the pump I hear a tick sound as the valve opens and equalizes pressure from the pump hose with the tire.
I may be wrong, but it works for me that way.