I have two different WordPress sites on different hosts exhibiting the same behavior since I upgraded to 3.2.1. Now if I try to update themes or plugins, I always get:
You don't have permission to access /wp-admin/update.php on this server.
I removed (temporarily renamed) all .htaccess files to make sure they weren't causing problems. I checked the permissions of that file (644) and they look good.
Any ideas what might be going on?