It is possible to get severely degraded performance if the add-on cards are not placed into the correctly rated slot. (x4, x8, x16).
This can indeed be reduce throughput of disk system connected through a PCIe (PCI Express) based controller if the card is placed in a slot with lower capacity than the card can support, e.g. x8 placed in x 4 slot (most high speed disk controllers appear to be x8) and is especially complicated by the fact some Dell systems have what look like x8 slots but only half the pins are wired so it's a x4. You need a torch and a sharp pair of eyes to read the motherboard.
http://en.wikipedia.org/wiki/PCI_Express
But I'm inferring that the disk system of the original poster is using internal disks connected to the pre-installed Perc controller which will therefore be in a slot that is the correct capacity. The basic throughput of copying a test file semi-confirms that it's unlikely to be the disk system of either end or the network that is causing the bottleneck. Not completely eliminated though.
The fact that it's using RAID-5 won't be helping compared to RAID-10. RAID-5 imposes quite a considerable overhead per write (x3 is some cases):
http://en.wikipedia.org/wiki/Standard_RAID_levels#RAID_5_performance
It appears to get worse with random writes which I suspect happens a lot in a deduplication system database.
We're using a SATA-II RAID-10 array which introduces potentially more failures (SATA disks have lower MTBF/duty cycle than SAS), lower spin speeds and 3GB/s transfer. However, the improved performance of RAID-10 goes a long way to offset the lower performance. The higher failure rate we think is acceptable especially as RAID-10 is more resilient to multiple disk failure than RAID-5. When we upgrade the disk enclosure, we'll be putting 3TB x SATA-III in there which takes away the performance angle.
But considering that BE can only manage 1000MB/min (see screenshot) on a good day on a disk system that can also manage a peak copy speed of 6000MB/min means that overly worrying about disk performance isn't going to really get us anywhere.
TIP: we get *much* improved disk speeds to the same disk system when we use a B2D target - can peak at around 3,000MB/min which is better than our aging LTO-3 tape system. Try doing some speed tests with a temporary B2D target and see what you get. If it's still rather low, then it does point to something outside of BE.
Cheers, Rob.