Appellations
When she calls him Sir, she's upset. He hates to hear "Yes, sir."
When she calls him Father, it's business as usual. He's grown to expect a bright 'hello, Father' when he walks into the kitchen for breakfast. When he calls her, 'yes, Father' floats down the corridors.
Sometimes, she calls him Old Man, despite his protests. He's only middle-aged, after all. When she's in high spirits she dashes into the console room and pokes herself into his work, looking at him upside-down as he works in one of the under-stories of the TARDIS, her white-blonde hair swinging. "Hello, Old Man!"
In danger or negotiations, she uses his name. It's strange to have his own child call out "Doctor!" But not everyone they meet needs to know what she is to him.
She had called him Dad the day she was born. And she's never used it again. Why he notices that he doesn't know. A Gallifreyan child usually addressed parents in formal, proper names, names that encompassed the respect of the child for their elders. Father was actually rather informal by Gallifreyan standards.
But Jenny isn't a Gallifreyan child. Jenny is his daughter. All the rules are out the window in her case.
And he is her dad.