Thanks for the help, I took a look in the root/ispconfig/httpd/conf file and found.
# This may also be "None", "All", or any combination of "Indexes",
# "Includes", "FollowSymLinks", "ExecCGI", or "MultiViews".
# Note that "MultiViews" must be named *explicitly* --- "Options All"
# doesn't give it to you.
Options FollowSymLinks MultiViews
# This controls which options the .htaccess files in directories can
# override. Can also be "All", or any combination of "Options", "FileInfo",
# "AuthConfig", and "Limit"
# Controls who can get stuff from this server.
Deny from all
I thought the deny looked a little odd and changed it to Allow and now I can access the admin area again. The only thing that concerns me is that I don't remember changing it but I might have while frustrated with trying to get Magento working in ISPConfig. Is this a security risk to leave set at "Allow"?
As far as funning ls -la there is no .htaccess file in any of the ispconfig directories... I've searched all of them.
Thanks for pointing me in the right direction.