Originally Posted by webist
I don't mean to be insulting. Perhaps the retainer nut is on the inside of the rim because it wasn't removed when the tube was installed? That would make the stem quite a bit shorter. I've seen people forget to remove one before.
I like this suggestion! I don't think it's the right one, since this is not a bike fresh off the lot... but it's a great explanation.
I have often had problems with small hand pumps not getting the right grip on a presta valve, and ironically, the worst seem to be the pumps designed for Presta. I have a magic multi-valve pump now that works fantastically, except that it's very small and I need to pump it 300 times in order to get the tire full. Anyway, the point was, I'm betting that without the nut on there to hold the valve steady, his pump is just not getting the grip it needs.
The other problem I have had with presta valves is that little doohicky that you unscrew to open the valve, the metal one under the cap... sometimes that gets bent a little or positioned at just the wrong angle (it's a little loose, in order to admit the air) such that the pump has a hard time pressing it into the open position and a certain amount of wiggling is required to get everything aligned just so.
Overall, I like presta valves... they seem sturdier than the schraeder's that used to cut themselves on the rim of my tires... but presta is a fiddly little mechanism; not the easiest to get right. My conclusion: the OP is just not getting something right. I hope after his trip to the LBS he tells us what the answer to the mystery was.