Right now, this flag appears to be generated whenever three questions in a row are closed. It's even a bit extreme - if a user asks 10 questions and the first three ever asked are closed, it appears to get generated even though the 7 more recent questions are not closed.
The age of the questions should be considered. It should look at a rolling window of user questions for raising the automatic flag. I don't really care if the user's first three questions on the site were closed if there are a number of other good questions. Perhaps only consider questions asked in the last year or maybe 3 consecutive from the last (n > 3 questions, I'm thinking n = 5 or n = 6 would be good) get closed.
Consider user activity. If the user isn't active on the site, I'm not going to do anything other than dismiss. There's no need to notify someone who doesn't participate any more about their poor participation. If the user hasn't been active in some period of time (3 months? 4 months? 6 months?), don't raise the flag.
Some closure types aren't necessarily bad. Duplicate questions should not raise the flag, although perhaps a large number of duplicate closures should raise a different auto flag. Migrations (especially with all the SE sites - I can't even keep track of them sometimes) also shouldn't count toward a closure flag, although perhaps a large number of migrations should again trigger a different flag case. For example, a unique flag after 3 migrations or a unique flag after 3 duplicates would be acceptable, but this should be a different flag than 3 closures for what generally amounts to low-quality questions.