I have a private client testing server set up and for some reason all the links work except for magento connect. For example.
http://myserver.com/clientname/ (is the root for the Magento installation)
When I click on Magento Connect from the admin panel it redirects to this site http://myserver.com/clientnamedownloader
Now every other module/page seems to work and nothing seems abnormal in my .htaccess file and the correct permissions are setup for the folders.