Mass downloaders causing mass errors

Not sure if this should be cause for my concern. I’m getting numerous errors -client denied by server configuration- that appear to be caused by the programs that download entire websites for offline browsing. I’m wondering if my directory and file permissions should be allowing or denying these people access to the plugins error logs and other files. Also, after upgrading to WP 2.2 I no longer receive the update announcements for plugins in the plugin control panel or admin dashboard. Permissions are set to 755 and 644 as they have always been for the 2+ years I’ve been using WP. By the way, WP has worked perfectly for my site the entire time.