If you are going to back up a GroupWise NetWare server remotely, then you need to have the Client Agent for NetWare installed on the remote server if you want to backup via IP. If the Client Agent for NetWare is not installed the backup will be done via IPX.
I'm currently using the gwagent on a groupwise server, have had a lot more problems with the agent since upgrading to arcserve7. Arcserve 7 is suppose to work under IP only..it does but not very well from what I've experience.
When you say 'not connecting' do you mean that the manager does not see the server or you can't connect to the agent.