The Magento Connect uses values stored in the directory downloader to know where to connect, where to save files etc. The problem is that these paths are hard coded into files at the installation of Magento.
If you wish to move your installation to a new path then this will break the Magento Connect in the admin panel.
The version that I find easiest to do on the new server is to log in using ssh and then run “./pear mage-setup .” That will reset the aboslute paths that are stored in the downloader directory.
Another option would be to re install magneto: