James Huff on "Delete all comments"

When Akismet flags something, it goes into the Spam folder. If the comments you're referring to are just going to Pending, it's not Akismet.

Double-check your comment moderation settings at Settings -> Discussion in your blog's Dashboard.

Pay extra close attention to the number of links you allow, as the Website field counts as 1. So, if you only allow 1 link, anyone else with a link in their comment and the Website field filled in will count as 2 and therefore be held for moderation.

Also, pay extra close attention to your comment moderation list, as it works on word parts. For example, and please excuse the follow word, if you add "ass" to your moderation list, it will also hold comments containing "class," "pass," "grass," etc.

via Chebli Mohamed