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Originally posted by: Darth Chaltab
Vader could always sense her in the Force, he just never knew she was his daughter.
I doubt Padme was strong enough in the Force to leave an imprint Vader would notice, and he might have forgotten Padme altogether by then.
There are still inconsistencies overall, ie: God help me I'm actually goint to cite PM, but Qui-Gonn's whole basis for trying to get approval to train Annakin is that he senses how strong the force is in him. Also, in ANH, when Vader and Luke are racing down the trench in the battle of Yavin, he says "The force is strong within this one", which at least implies that he's been able to sense a presence in the force in other people in the past.