So she's reading RotK solo, no help, and getting through and understanding it? I doubt my MG 3rd grader would do that. (I mean, maybe, but Tolkien is dense, and also rather dry.) She certainly wouldn't read Shakespeare. Your DD normally chooses to read at that level?

She does 4th grade math workbooks with little/no instruction?

It does seem that something must be quite off with the testing, then. It's just odd that we don't see at least an occasional peak, though there are a few 99s in there.