"Am I not really her son?" is the question at the root cause of a two-year long pain.
It first started with a small seed in Shaun's mind. Am I a synth? He had no reason to think this, he blamed the thought on common wasteland paranoia. And he excused the thought on the same reason.
Shaun had been in Sanctuary for two weeks the first time Sturges told him he was a synth. When Shaun asked how he knew, Sturges tells him: He couldn't age, he couldn't remember parts of his childhood.
That struck a chord with him. Shaun couldn't remember any parts of being younger. But that's easy to explain, and he can come up with many excuses for why. Not aging, though, would take time to prove.
Flash forward to one year; he's eleven, and he would swear on his life that he doesn't look any different. He wouldn't have noticed this too much if Duncan, his step-brother, wasn't growing like crazy. Duncan had lost two baby teeth, and had grown several inches. His mom would mark their heights on the door frame of their room. Duncan, growing slightly every few months. Shaun was stuck at 4'8".
He fears if he were to bring this up to his mom, he figures he would be struck with a 'late growth spurt' talk. And he does not want to talk about growth spurts with his mom. Gross.
Now he's turning twelve. It's been two years since his mom and the Minutemen destroyed the Institute. Sometimes, he'll think back to the first time he met his mom. In the Institute. It is a downright weird story of how they finally were reunited. His kidnapping, how she overcame losing her husband—his father—and saved him and the Commonwealth. And the coolest part of the story; how she survived the bombs. He guesses he did too, but Shaun doesn't remember it.
Shaun would never tell his mom about feeling that way, having that question. Not for a second has he thought he's been brave enough to bring it up.
But after all this time, he still wonders: "Am I not really her son?"