The problem that has caused comments from regular readers to be treated as spam should now be resolved.
For the information of other MT and Akismet users, it relates to how MT handles multiple spam tests. MT-Akismet assigns a score of +/-6 to each comment, then the e-mail and URL fields are checked against past comments in order to establish trust. You used to get a score of +1 for previous publication of your e-mail and +1 for a URL.
The problem arose at the next step, where the total score is averaged across the three tests. MT doesn’t include zero scores in this, so the following bug results: if you get one point for each of the trust checks, and six from Akismet, your average score is +2.67, which is below the trigger level. If, however, you had never commented before, rather than divide the 6 points from Akismet across the three tests, MT disregards the zero scores, so you get a final score of +6 and instant publication.
The workaround is to increase the scores for links and e-mail to 2.