check if you have multiple interfaces in your master and media server.
A new feature in 6.5.x is the use of pbx_exchange. This service will discover all NICs installed on the host, and register/broadcast it.
6.5.2 will look at this list and do reverse lookup. Then check the hostname against bp.conf file (or server list in the registry), then if listed NBU NEW processes such as nbpem, nbrb, nbemm, etc who communicates via CORBA/pbx will automatically use any one of these interfaces to connect. This is in a way a good thing.
BUT there are a BAD side to this.
If you list all the interfaces in your bp.conf file, and not every one has connection to the master server, or to another media server which it shares drive with; AND if that interface is automatically selected for communication, you'll have to WAIt there until it times out before pbx determines another interface to try.
This requires looking at bp.conf maintainence a whole new way, you'll have to make sure your SERVER and MEDIA_SERVER lines do not include interfaces you do not wish NBU to communicate out of on each hosts. Otherwise any one of them are candidates.
So to be clear, if for example you have a host with 10 NICs. But only 5 are in used for NETBACKUP, and the media and master can only talk through these 5. You should add these 5 hostnames to bp.conf file, BUT not all 10.
To speed up and add some resiliance to do reverse lookups, you can employ /etc/hosts for each of those IPs as well.
This might improve things, and even if you have a different issue, hopefully this will prevent another.
P.S. Though 6.5. is backup compatible with 5.x media servers, it is HIGHLY recommended to put all SSO media server to same version.