I think that, obviously, during S2 they were still getting to know each other. For me, I always use Aiden. Flack was obviously close with her, and during S1 he and Aiden worked a lot of cases together. I think they had a little bit of chemistry. Flack might've seen Lindsay as Aiden's replacement, and resented her for it. You know, tried to find something wrong with her, and not even tried to get to know her. But I think "Cool Hunter", the first case they worked together, was when he realized that maybe he should give Lindsay a chance, that she might not be as bad as he's been trying to make her out to be.
"Charge of This Post" we saw them flirting so bad, and obvious chemistry again. I mean, that whole block party thing? Ugh. And the way they looked at each other... Yeah. They were totally crushing. But then Flack went 'splody, and Lindsay realized that hey, she really likes that tall good-looking cop. And maybe it scared her, because she was never supposed to like Flack. She was supposed to like Danny, because from day one that kid's been flirting with her even if he didn't realize it.
During Flack's recovery they grew closer. She went to see him in the hospital, and when he got out. The conversation in "People With Money" was so choice. It was almost like an inside joke. And then the way he looks at her -- like in "Not What It Looks Like", in the bank and when Lindsay went UC. Flack looked so worried, he had the radio up to his mouth like he was just waiting for a chance to go save her.
As of "Raising Shane", though... Hm. I think they're dating. Yes. Why do you think she didn't show up for her 'date' with Danny in "Love Run Cold"? Obviously she was with Flack. He told her how he felt the same night Lindsay went UC, and now they're treading the tepid waters of love. xoxo.