Here's what I think's happening:
If I enter anything at all into the Comment Blacklist while Akismet is enabled then every comment is sent straight to Akismet. This happened to on WP 1.5 and now on 2.0, with far fewer plugins. Before I start disabling anything and everything, can anybody confirm that they have entries in the blacklist, plus Akismet, and everything works fine?
Only asking because there are some banned users I'd really rather have deleted straight away rather than moderated!