Since you startled her the last time you spoke up while she was deep in thought, you reach out and tap her shoulder

Please stop that. She says flatly, turning to affix you with a disdainful gaze

Please remain professional during work hours, Professor. It's inappropriate, and I need to concentrate on this.

She knows you didn't have any intent to harass her, but she still wants to keep her distance. Maybe she still doesn't fully trust you, or maybe she's suppressing some other emotions