Backing to a null device using media agent from the cell manager was the same.
Backing to null device using media agent installed in the fileserver helped improve the backup performance. But wasn't impressive either. For instance, the first case it took 20 hours to backup 90 GB and in the second case, it took over 4 hours with throughput 6.9MB/s. Old version of Backup Exec running on that machine did a better job.
So, I enabled two other NIC ports in the server (different network card) and assigned them to the backup VLAN (previously it was being backed up through the production network on a different VLAN). Teamed the cards and gave it a different IP. Created a new DNS record for that IP. And imported that DNS name as a Virtual host to the list of clients. Modified the backup spec to select the new imported client instead of the old one. Ran the backup job. The same thing @ 1.06 MB/s.
Apparently, the data is not being pulled out from the new interface. NetIO between the cell manager and fileserver with the new interface works good. This POS software is not sucking the data from the NIC it is supposed to.