I recently had a problem on one of my blogs. Unfortunately it took me a while to understand that it really was a problem, but then I noticed that all comments made to my blog were immediately tagged as spam in WordPress, and thus I did not even notice that comments were made, and after 15 days they were deleted from the spam folder.
As I found out I quickly made a search in Google to find the solution, and in the first post I found the solution (for me) was found. The person wrote that he had to disable his Anti-Captcha plugin, and once that was disabled, the comments started showing up again (former comments remained in spam queue or deleted, but new comments will start showing up again). That did it for me. If you suffer from a similar problem I recommend that you disable different plugins, especially anti-captcha plugins if you have them, and see if that will help you solve the problem!
In my case the interesting was that Akismet cleared the commet, saying that it was not spam, but still it remained in the spam filter. This is what it looked like:
1 min ago – Comment status was changed to spam 1 min ago – Akismet cleared this comment
Hope these instructions have helped you, and good luck and have fun blogging, commenting and accepting comments made to your blog!