I could see this being a problem with a Local RAID array on your machine, but I doubt it for backups over network. Backupexec has no clue that the remote even has an array, it just sees a Samba share.
What version of firmware are you using ? The machine running Backup Exec, is connected to the network with Gigabit or 10/100 ? Is it Auto or Manual forced.
On your DNS343, Speed 10/100/1000 (auto or manual set) ? Are you using a managed or unmanaged switch ? Jumbo frames enabled ?
I would suspect more a network issue. I have had a few issues trying to stream media to units like my WDTV Live, when Jumbo frames were enabled. Since the WDTV Live is conencted at 10/100, on an unmanaged switch which doesn't do
BTW: What kind of drives are you using ? I had a problem on my QNAP TS409 when I tried using a set of WD Green series drives. I had used a set in the past an had no issues, but with another set, I could never transfer more than 400 to 500MB without the unit timeout out an choking. I switched to some hitachi 7200 rpm drives, and the problem disappeared. On 1 of DNS343 units, I am using Seagate ES.2 drives, and on the other one I have a set of Seagate Constellation drives. My Synology DS508 is using 5 Seagate 2TB LP drives.