could you implement the setting of the proxy via an “Automatic proxy configuration URL”, like IE or firefox can do it.
In some company or university networks there is no other way to connext to the internet for updates.
As soon as we will switch to Eclipse 3.4. this option will also be available under “Window->Preferences->General->Network Connections”. In Eclipse 3.3 the automatic proxy configuration URL option is not available. In the meantime a possible workaround would be to download the update site and update KNIME with the “New Archived Site” option of the update manager. Then you have to go via Help->Software Updates->Find and install…->Search for new features->New Archived Site. Select the downloaded zip file. Let us know if that worked for you.