What's gone wrong here? This is unacceptable!
This post on Meta Stack Exchange suggests that when you vote to close a question, any flags you also raise on it are nulled, to prevent an unnecessary (and exploitable) increase in helpful flags:
I assume that this has been extrapolated out to answers and that you cast a delete vote as well as raising the flag? This would likely result in the flag being recorded as 'none' to fit the pattern Jeff describes for questions.