Palps replies "Search your feelings, Lord Vader, you know it to be true."
RotS finally made sense of that change. Palps new Padme survived and gave birth; Vader did not. Until Splinter of the Mind's Eye, that is. Vader must have figured out that Palps lied to him about him killing Padme and then tried to hide his knowledge of Luke from the Emperor until he could seduce Luke and over throw Palpatine.
But of course, that didn't pan out.