Thing is, I don't have an .htaccess file ANYWHERE on this system. I checked.
If you don't have a .htaccess file, then why have the AllowOverride directive in the .conf file?
Putting AllowOverride in means that every time apache retrieves a file from that directory, *and every directory below*, it will look for a .htaccess file in the current directory, and every directory above (until it reaches the original directory). It doesn't cache the information (because it can change), so it means a significant increase in the amount of disk activity for each page. It also provides another attack surface for naughty people.
So in general if you don't use, or intend to use, .htaccess files, then don't put in the AllowOverride directive.
P.