It is not the first time this happens. It might be a good idea to merge the comment trees and let both links show at the top of the page for these cases.
No, but in the case where there are two posts covering the same story on the front page, it's certainly a factor.
If one url had been obviously better than the other, we would have kept it and (if necessary) assigned it to the thread with more comments. In this case, neither url was obviously better. That's why I asked, and also why the responses were contradictory.
Edit: since this thread has all the discussion, we'll keep this one.