After a couple hours there are often far too many comments for a moderator to read them all. This means that comments made later in the discussion, including ones that correct previous highly rated comments, don't get a chance to get moderated up. Many intelligent commenters can only check the site once a day, and are thus discouraged from making comments that will be buried under a thousand posts of noise.
A possible solution is to allow every reader to recommend any comment, but only show these recommendations to readers with mod points. This would enable moderators to spot and evaluate the valuable comments added late to the discussion. This would especially help excellent anonymous or plus one posts make it up to the critical level of 3, which is extremely difficult when posted late.
Another possibility would be to give moderators twice as many points, but only allow the extra points to be used after maybe the first hour or two. The later points could be applied to a second score instead of the original score. So each comment could have two scores, a first hour score and a late score. This might be combined with a system where comments are limited to 5 during the first hour, but could be raised to maybe 7 after a couple hours.
It's also common that even a highly rated post with especially valuable info is stuck way at the bottom of the page where one can waste a lot of time reading down to it or never get there. Perhaps there should be maybe five comment slots at the top of the page reserved for the highest rated comments to be brought to the top. This would also help reduce the temptation to post in an off topic thread at the top of the tree in order to prevent your post from being pushed way down the page.