This is very odd. I noticed it today, but it5 might be the result of the upgrade to WPMu two nights ago.
when I open my main blog, http://blogpeoria.com
All the links on the resulting page have been pointed to a corresponding page on a member blog: http://peoriawatch.blogpeoria.com
For example, {url]http://blogpeoria.com/2009/07/10/changes-to-the-terms-of-service/[/url] instead points to [url]http://peoriawatch.blogpeoria.com/2009/07/10/changes-to-the-terms-of-service/[/url]
This is the link I see when I hover my mouse over these links.
When I first notices this, the front pager blog had switched to the theme the Peoria Watch blog was using. And the front page was renamed to the name of the Peoria Watch blog.
Also, on my admin pages, the "WPMu 2.8.1 is available" message is still showing.
Also, all the mu-plugins have been deactivated by renaming the folder.