As much as Sam hates that she looked at Pete and saw her last chance, she hates it more when she looks at Jack and thinks lost cause.
He's her friend and her CO and is important to her for a hundred reasons, but everytime she sees him across a desk or on a video link or being beamed in 3d from the Prometheus, Sam has to take a second and orient herself.
It wasn't supposed to be like this, the part of her that was raised on adventure stories and fairy tales nudges her. The hero is supposed to get the fair maiden, and if in this case there is a little gender ambiguity and the person figured as the fair maiden is actually a hero in his own right, well, there's nothing wrong with that.
But still. There's that same little part that thought when the time came for him to leave the Stargate program it would be for her, for them, for something that would put them on equal footing and allow her to make it plain what she wants.
But that didn't happen and she doesn't know why and she's tried to tell him what she wants, which is him, just him and no titles and ten minutes without some one walking into hisoffice or popping around the corner or demanding that she or he or they save the world. She's tried telling him that one too many times now and if he hasn't exactly made himself clear, he's just too unwilling or unable to open himself up to her even a little and she is too full of pride to take another not-quite-panicked-but-something-scared rejection or refutation or refusal to hear what she has to say.
So Sam looks across the briefing room table and the video link and the 3d projection and lets herself mourn the last little bit. Pete might not have been her last chance, she thinks on her more optimistic days, but she can't help but file Jack safely away under lost causes.