playandlearn,

I have a DS11 in 6th grade who is in his first year of middle school after having been in a gifted magnet for elementary. Even in the large circle of gifted kids, most of the boys don't get him. By and large, with a couple of exceptions, his closest friends are three girls from his gifted class in elementary who love his quirks and he likes their qualities which are, in turn, not always appreciated by girls in middle school. In other words, they "get" each other.
So perhaps your DS could expand her search for friends and see if there are boys who would appreciate her wonderful qualities. Good luck to her and you! Middle school is certainly tough so far.
Please keep us apprised of how things are going for her!