Jim Kirk—Captain Jim Kirk finds everyone aesthetically pleasing. Let's be honest he is a slut or at least she perceives him that way. The man would hit on your grandmother if you introduced her to him. Actually he would probably hit on your grandfather too because he doesn't feel like limiting himself to only half of any species (including half-Vulcans).
The first time she met Jim, he made a pass at her. (This became a normal behavior pattern until he found a new target, unfortunately.) There was also the fact that three years later he slept with her roommate just so he could win the unwinnable test. Last week he secured mining rights from a particular planet by spending 30 minutes alone with a certain ambassador doing who knows what.
Therefore it does not surprise her that she catches her captain checking out her boyfriend's ass on the bridge. She's not even surprise when it starts becoming a regular occurrence. (She does find this highly frustrating, but at least he's no longer looking at her ass.) She is also not surprised that her captain becomes a master of double entendres around her boyfriend that Spock supposedly doesn't understand.
What surprises her is that her captain is attracted to her boyfriend even though they appear to hate each other. They are always fighting when they are not doing something work related. Actually they are always fighting even if they are doing something work related. It doesn't matter because they still work well together regardless.
Eventually, she realizes that they are not actually fighting with each other. This is just how they communicate. They are really not fighting, just talking with passion. For some unknown reason her boyfriend and her captain are able to communicate with each other on a level that is completely unique to the two of them. Even though she is a communications expert she still doesn't understand what's going on completely.
The fact that her captain can make her boyfriend feel anything passionately is an entirely different issue. (See sign one of her other rant regarding her boyfriend and her captain. Yes her boyfriend and her captain are driving her so crazy that she must do two separate rants or risk strangling the two in a non- sexual way.)
What truly let her know that something is different this time is that her captain enjoys arguing with her boyfriend too much. (No, she is not referring to the rumors about her captain having a choking fetish or a half Vulcan choking fetish. She refuses to talk about how this rumor started after surveillance footage of a certain bridge incident started floating around the ship.)
No she is talking about the fact that when they get into an "argument" her captain is usually smiling the entire time unless the situation is truly dire. She realizes quickly that her captain gets a certain amount of "pleasure" from triggering an emotional response from her boyfriend.
At first she mistakes this for Jim's normal smug approach. She knows better now. He is not just "arguing" with Spock purely for pleasure. Actually it is still for pleasure but it's a completely different type of pleasure. (Apparently her captain forgets that her boyfriend is her boyfriend.)
This is when she comes to the revelation that her captain is not arguing with her boyfriend. Her captain is flirting with her boyfriend. This isn't his normal flirting. He actually likes her boyfriend as more than just a conquest.
The thing that makes her realize this is that her captain avoids certain subjects in her boyfriend's presence. He never triggers an argument with mention of the destruction of Vulcan, the death of her boyfriend's mother, or the "bridge incident." He will not even mention the "bridge incident" as a joke. He actually goes out of his way to be sensitive to her boyfriend's emotional needs. (Yes, contrary to popular belief her boyfriend does have emotional needs. Unfortunately, only her captain and she are aware of this.) The most notable example is that even though her captain calls everyone by their first name whenever possible he refers to the three women on ship with the first name Amanda by their last names only.
This fact in itself gives her cause to believe that maybe her captain is more than just attracted to her boyfriend in his traditional way. In an effort to preserve her relationship with her boyfriend she decided not to point this fact out to either party. If they can't figure it out on their own, she won't tell her boyfriend or her captain. She will ignore this information unless her captain does something truly idiotic.