Check you NIC utilization during backups and AuxCopy operations. If it is showing almost no usage compared to the amount of data trying to go through it then this solution may apply. Note you will usually only see this slow down when more then one job is running.
When troubleshooting throughput issues of backups going to Data Domain devices have the customer check to see if ntfs-acls is enabled on the Data Domain. Disabling this option has been confirmed to fix throughput issues on two separate cases.
There's a new option in version 126.96.36.199 of the Data Domain OS called ntfs-acls. Having this option enabled (default is enabled) causes a lot of overhead when running multiple backup jobs, and causes extremely poor performance. The solution was to run the following commands on the DDR:
cifs disable cifs option set ntfs-acls disabled cifs enable
"We can now run multiple backup jobs to our DDRs, and the MediaAgent NIC throughput is over 95%. "