I got this “A server or network problem prevented Akismet from checking 1 comment…” message today, too. But it doesn’t seem to go away, i.e. after the displayed minutes, it just starts its countdown again. (While other spam comments still get successfully marked as spam, so it’s no permanent connection problem.)
Some hours ago, I had received a standard “please moderate” mail for a typical spam comment with many links – so seemingly just one that Akismet didn’t catch – and clicked the link to mark it as spam. Only after that I noticed this problem message for the first time (having installed 2.5.0 the day it was released). Some time later, I deleted all the spam that had accumulated with the “empty spam” button, but the problem message persists. Is Akismet trying to re-check a comment that no longer exists? And if so, how to turn this message off? (Even if it means editing a database entry.)
On another note, I noticed that my wp_commentmeta table is filling with hundreds of akismet_* entries, mostly akismet_history and akismet_result. That’s obviously related to the new features – but I hope those will be expired after a certain time and not flood the database with eventually tens of thousands of entries… will they?