The Windows XP SP2 system should have the remote agent installed on it. All Windows 2000 Professional and Windows XP systems can be backed up without need of a Remote Agent license. So for that system it will need the remote agent even if it worked under BE 10.x.
For the NetApp Filer you may need to disable NDMP for this to work. The version of NDMP used by BE changed for BE 11 so this could be the reason.
The system with Samba, technically we didn't test past samba 3.0.23c (listed on the SCL) but I tend to doubt the minor changes could prevent backup and restore.
The UMI of V-79-57344-3844 maps to the following error:
The media server could not find an appropriate port to bind to. If a port range has been specified, make some ports in that range available.
I would suggest installing ethereal on the system running samba and see if it gets any connection attempt.
I would also suggest installing ethereal on the BE server, rather than use NetMon, and see what kind of response is returned to the BE server from the remote systems.
Ideally you will find out that either BE is never getting to the remote systems or the reply is not making it back to the BE server. Once it's narrowed it should help direct the next steps.
Other things to consider, since the error maps to ports, open up the firewall / gateway between the systems.
You may need to place the BE Job Engine service into debug mode to get additional information.
http://seer.entsupport.symantec.com/docs/275639.htm
How to Enable Debug Logs using BEUtility feature of Backup Exec 10.x and 11.d for Windows Servers.