1. I do not understand why Susan behaved the way she did. She drank a bottle of vodka and killed the cat. It is very surprising, she is generally a good girl. -> normally her behaviour is good -> we would expect good behaviour from her.
2. I know that Lara stole some money, she is a generally good girl. -> although sometimes she may be good, sometimes her behaviour is poor/bad -> we can usually expect good behaviour but not always.
1. is usually said with some surprise; 2. is usually said to explain or excuse bad behavior.
In 1. the emphasis is on good
In 2. the emphasis is on generally
If you have to choose between the two for exam purposes you should opt for number 1. It's really hard to say exactly why. I would not say: "She is a generally good girl", although Paul has provided a good example of where it could be used. On the other hand, it is idiomatic to say: "She is an exceptionally good girl". Think of it this way: "Generally speaking, she is a good girl". However, you wouldn't say: "Exceptionally speaking, she is a good girl".
Note, also, Vic's comment about how the adverb modifies the adjective.