Strange 'Permission Denied' message when browsing to CiviCRM home page
The errors in your log that you note are not a problem, they are CiviCRM doing a little security check for you (and succeeding).

I've seen this occasionally on my servers, and especially on my staging server. I believe that the cause is indirectly related to the errors you are seeing, in that:


If you're logged in, CiviCRM does a fair amount of these checks before rendering the page.
If you have production-type settings on a not-super-fast server, then you can get timeouts of various flavours that aren't necessarily going to show up in your apache/webserver logs.


As you probably also experience, just reloading the page will solve the issue, presumably because CiviCRM and or the webserver is using some kind of caching so it doesn't take so long.

In my case, extending the default backend timeout in my varnish configuration eliminated the problem.