Honestly, I think Jack called Miranda that for two reasons:

One being that she was basically the poster child for Cerberus. She basically always seemed to be singing Cerberus's praises all the time, espceially in the beginning. She was TIM's 'favorite' so to speak, doing whatever he asked of her. So, in a way, she was kind of like the cheerleader for Cerberus, trying to get people to agree with her and see that maybe they weren't as bad as their reputation seemed.

Two being that she was genetically designed to be perfect. She is gorgeous, intelligent, has the air of being better than everyone else. It basically screams cheerleader when you look at her in Jack's point of view. Jack had a dark past, and has kind of a dark attitude to go with it, so seeing someone perfect like Miranda would definitely harbor a bit of bitterness there. She had never been seen as perfect, always abused and experimented on, and to see someone who had a life and was engineereed to be perfect might have trigger some kind of jealously, maybe, Jack knowing she could never be perfect like Miranda was.

Poor Jack!