When I updated to 2.6.2 one of my blogs developed the problem of not showing the home page when visited by the 'raw' URL without a page file name - http://www.cryptosmith.com didn't work, but http://www.cryptosmith.com/index.php DID work.
My blog had a bunch of plugins enabled, including SuperCache.
The problem: My ISP tracked it down to a problem with my .htaccess file but didn't know what was putting bad code into that file. Apparently both WordPress itself and SuperCache put data into that file.
Resolution: I made sure I had updated SuperCache to the latest (post 2.6.2) version. I also deleted the old SuperCache contents from the .htaccess file so that the plugin could write revised contents into the .htaccess file.
Apparently the problem is caused by an inconsistency between the code SuperCache puts into the .htaccess file in the old version and how things work with 2.6.2.