Your sweet pup is so lucky to have been found by you...good job with her rescue and progress toward good health. I agree that it doesn't sound normal but I have nothing to share from experience. I'm thinking that the malnutrition affected her growth...a chance that her mother wasn't properly nourished while pregnant, either, and that she was negatively impacted even in utero. It's good that the vet says she's healthy now...my guess is that you just keep on a slow path to have her gain/regain her strength/stamina. Guess.
The board slows down a lot on weekends so you probably won't get much feedback till tomorrow or Tuesday.
My mutts and I welcome you to the board. (Sunnie rescued pregnant but seemingly adequately fed in the shelter, though not properly for being pregnant.)