I don't think I've flip flopped on story elements. Sometimes I've liked something and it gets better with re-readings but I've never disliked a story and then really enjoyed it another time.
It has happened with artwork though. Used to absolutely hate JRJR and then one day I read something he'd done and just got it all of a sudden. Same thing happened with Dark Knight Returns, liked the story but didn't like Miller's work on it. As time went by that period of Miller made sense to me and I started to really appreciate that version of his style.