The first time Maura realises that she has feelings for Jane is after the whole episode with Jane shooting her father. The time they don't speak hurts her more than she will ever be willing to admit, but she's also so angry with Jane that she can't just let her back in just like that.
Once they make up though Maura realises that she really doesn't like life without her best friend. She doesn't know how to say it, and doesn't know if Jane will even accept it, so rather than risk their friendship she stays quiet, doing her best to keep her emotions in check.
She slips up occasionally though, but Jane never seems to notice, and their friendship continues on. Maura waits though, waiting for the right time to tell Jane exactly how she feels, and until then she's happy to sit on the sidelines and watch as Jane lives her life.