I ran into a recent problem with Magento on a Windows/IIS install. From the admin, the I couldn’t navigate to the ConnectManager; instead it bounced me to the 404 page.
Confident that a fresh install can’t be quirky, I paused and thought it had to be a permissions issue. I opened the folder, checked the permissions, and IUSR_<
If your having problems with Magento ConnectManger, double-check the permissions on everything. And remember, if it’s a remote host, FTP may not be setting it as you expect.