Does your boss know that you had one-on-ones with all your reports to discuss your management style and rapport and have tried in earnest to address this situation with him and everyone? That is important for them to know.

At the end of the day, it doesn't matter if you're micro-managing this person or not. What is of concern is if you're doing anything that can be construed as illegal discrimination/workplace harassment OR if you have a poor relationship with multiple reports – both those situations would make you a liability to the company as a manager (and employee).