It may have been that Mama Kate simply didn't want Harry Kim to grow up. Case in point: The Disease. Janeway gets really angry about an offense by Harry Kim that she probably would have had an easier time accepting of other officers. She even admits this in the dialog.
So, perhaps she didn't promote him before that time because she hadn't fully realised herself she had a psychological need to keep seeing him as 'the newbie', and perhaps she didn't promote him after that because, even though she now realised that he had grown, she couldn't do it too quickly after the permanent reprimand in his record and had to wait a year or two, three. By which time they got home.
KIM: You reacted like any Captain would.
JANEWAY: Probably. But I can't help wondering if my response would have been the same if it had been, say, Tom Paris instead of you. Oh don't get me wrong, I still would have been angry and disappointed, but I wouldn't have been surprised.
KIM: Because Ensign Kim doesn't break the rules.
JANEWAY: The truth is, Harry, I think about you differently than the rest of the crew. Which isn't to suggest that I don't care deeply about each of them. You came to me fresh out of the Academy, wide-eyed with excitement about your first deep space assignment. From that first day, I've always felt more protective of you than the others.
KIM: I appreciate that. But that was five years ago. I've changed.
JANEWAY: Yes, you have.
KIM: Maybe I'm not the perfect officer anymore.
JANEWAY: Maybe not. But you're a better man.
So, perhaps she didn't promote him before that time because she hadn't fully realised herself she had a psychological need to keep seeing him as 'the newbie', and perhaps she didn't promote him after that because, even though she now realised that he had grown, she couldn't do it too quickly after the permanent reprimand in his record and had to wait a year or two, three. By which time they got home.
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