I can't come up with another explanation. Here's what happens:
Usually, Akismet marks something as spam, the plugin checks it and trashes it (I have the settings marked to do that).
Occasionally, Akismet marks something as spam, but the plugin just leaves it in the spam queue.
Since the plugin is set to either trash a comment or marks it as not spam (back into moderation), nothing should be in my spam queue.
What's going on?