Update: the problem has now been fixed.
A bug in development versions of WordPress is causing some comments to be incorrectly caught as spam. The problem is in WordPress, not Akismet, and there’s no way for Akismet to prevent it from happening.
The problem only affects WordPress blogs running current development code. It does not affect other applications that use Akismet.
Technically-minded users can read the specifics in the WordPress Trac system.
We expect to have a fix in WordPress core soon, and deployed to WordPress.com shortly after.
This is probably a good opportunity to remind readers that Akismet is not necessarily the reason a comment gets caught as spam. The majority of complaints we receive about real comments being caught as spam were in fact not caused by Akismet at all – but by other spam filtering plugins or features. (Unfortunately WordPress doesn’t show the reason a comment was moved to the Spam filter, so there’s no easy way to tell which ones were put there by Akismet and which ones by something else).
In particular, the WordPress Comment Blacklist feature (Settings / Discussion) trips up some users. It lets administrators provide a list of words, IP or email addresses that should be blocked as spam. Any comments that match words in the blacklist will automatically be moved to the Spam filter – regardless of whether or not Akismet considers it to be spam. The blacklist matches within words, meaning that if you add a short string such as “ru”, it will block any comment containing the words “truth” or “fruit”, or any other word with the letters “ru”. And, since the blacklist takes precedence over Akismet, reporting those comments to Akismet as false positives won’t stop them from being caught.
If you think the Comment Blacklist feature might be catching legitimate comments as spam, the tw-blacklight plugin might help your diagnosis.
We’ll update the Akismet blog when the WordPress bug has been fixed.