This happens to me once in a while with a particular tube/valve. I think it is because the little presta pin is not releasing when I put the pump valve on- even thought I 'primed' it already by letting a bit of air out first. When it sticks closed like that I just have to take the pump valve off again, release a bit mnore air from the tire, and then the valve works ok. The problem goes away again when i eventually put a new tube and valve.