To be fair, we don't know exactly what happened with Noah that made him forget, but it must have been pretty terrible if he asked Rene to kill him if he ever showed up again, so maybe Molly thought she had a good reason to run.

They never showed Robin Masters you only heard his voice.

In the finale, Higgins tells Magnum that he's Masters. But at the end, he takes it back and says "I lied." It was a dumb plot point anyway, because as I said, Higgins had several private talks with Masters on the phone.