In A New Hope, Vader appears to have no lights at all on his box. In The Empire Strikes Back there are lights on the box but they do not blink, and in Return of the Jedi they blink.
I'm looking for an in-universe explanation, not just something about the movie's budget. :) I've read the Wookieepedia explanation of Vader's suit but I call BS on the whole thing. The way this entry describes Vader's weaknesses, he wouldn't have been effective at all following his injuries. That would completely negate everything in the EU which states how powerful he was and his further extermination of the Jedi. Besides, that entry doesn't address the light issue.