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It's hard to get the hang of it sometimes. But I think you're self-diagnosing right (i.e. not hooking the pump low enough on the valve).
One thing that might make things easier is prep the valve by letting out a bit of air. You unscrew the top part of the presta valve, you press it just a little, "pchhhtt pchttt" (you get the idea) and then snap in your pump head, lock, and pump away. When you attach the head to the valve, some air DOES go out into your pump (creating an air sound or not, depending on the pump), which allows you to read the tire pressure on your pump's gauge. When you pull the head out there should also be another very short air-rushing sound as air left in the pump exits (not on every pump for some reason).
Good luck!