It means that no every girl will care about it or think much about it. Think of it like counting. A girl counts how many times a boy is nice to her. But if he performs a certain action (example: buys dinner), it will not be entered into the amount of nice things she is counting. Like she is keeping a score in her mind. Hope that helped! :)
A different example:
I gave extra information on the exam, but it didn't count for extra marks. -Meaning he only got marks for the information needed. The extra information was not needed, and didn't count towards the final score.