Few factors that can affect the throughput:
The cache and supported command queue'ing of the HDD's will have an I/O impact. What is the manufacturer and model of your HDD's?
Jumbo Frames works best when all of the devices being used support Jumbo Frame and gigabit. Have you verified that you have the latest drivers and firmware (if applicable) for your PC network adapter?
Cabling (assuming they are self-made) may have an impact as well if they are rated to be less than CAT5e, not wired to standard on both ends (ex: 568A/568B for all connected cables), or exceed/fall-short of the approved lengths as excess error correction (collision) may be occuring.
Real-time scanning applications/services such as Anti-Virus, network services (bittorrent, streaming, etc.) also slow down transfer if they are enabled.
Cheers,