What was Margaery's motivation to call Cersei 'sister' again?

The balance of power had shifted considerably since the first set of quotes. King Joffrey is dead, and his younger brother Tommen is now king. Unlike his wild card of an elder brother, Tommen is gentler and more prone to manipulation by his new bride. The Lannisters impeccable image has also been shattered. They failed to prevent the assassination of their king in the midst of his own wedding day, and the suspected assassin is the king's Lannister uncle. Not only do they look incompetent, they are divided among themselves.

On the other hand, the Tyrells' situation is much stronger now. Tommen is already wrapped around Margaery's pretty little finger, and she knows that the assassination was orchestrated in part by her own family. In Margaery's eyes, the Lannisters look disoriented and lost. Putting on a show trial for one of their own, whom she knows is innocent of any wrongdoing.

Whatever power Cersei held over Margaery has now been diminished.

Margaery was testing the waters, so to speak. Having been rebuffed once and well aware of Cersei's violent streak, she is trying to find where both of them stand now.

The first time, in Season 3, Margaery was trying to play Cersei with her silver tongue and win her over. Now one thing we know for sure is that Cersei doesn't like to be played, by anybody at all. She is a strong woman who likes to be on top of every situation. She already has a pre-conception of Margaery and her manipulative ways and doesn't like it one bit. Least of all, the way Joffrey acts all putty in her hand.

Remember this was a time when Cersei was herself struggling with her relationship with Joffrey. These conditions had already set an air of unhealthy competition between the two women. This is the prime reason that Cersei takes Margaery calling her a "sister" as a slight.

However, now in Season 4, the bone of contention between these two has died with Joffrey. Cersei has grown slightly less distrustful of Margaery. She knows that the Tyrells are indispensable. As for Margaery, she is pretty confident of her and her family's position in the current scheme of things. She no more sees herself as subservient to Cersei. Quite the opposite, she is now her contemporary.

So when Cersei comes to Margaery in the said scene (rather than Margaery seeking her out as in the first instance), she senses it as a perfect opportunity to rebuild her relationship. I say rebuild because, this time she's treating Cersei as an equal and her tone is not sugary or condescending. Her gentle, prodding approach got her the desired result which her pretentious approach didn't the first time around.