I too have the same problem. I'm running WP 2.1 with Akismet 2.0. The plugin was working fine until just a few days ago when I noticed the number of spam comments was incremented (in the Dashboard) but under "Comments" menu, Akismet showed "0" in the queue. Clicking on Akismet showed nothing but the number of spam comments it had protected me from.
I did as "armymomnj" did and deleted and downloaded another copy of Akismet 2.0, uploaded and reactivated. Same problem. Akismet incremented (from 197 to 199 spam comments) yet Akismet still showed zero in the "comments" menu and nothing on the Akismet page.
I have no other spam comment stopping plugins such as Bad behavior or Spam Karma installed. Only Akismet, Simple Trackback Validation and Did-you-pass-math plugins. These are all WP 2.1 compatible and all worked without a hitch until a few days ago when Akismet began making my possible spam comments disappear. Oh...and I do not have the "Automatically delete comments on posts over a month old" checked either.
Bottom line: The new version of Akismet appears to be immediately deleting all possible spam comments it catches without any user intervention and no longer holds them in the Akismet queue as it should.
I initially thought it was not showing duplicate comments or comments from known (previously caught) spam addresses. Could this be the case?