Data Deduplication

I'm running Win7 Pro on my desktop and have an EX490 with the factory 1TB hard drive and 2 1.5TB WD Green drives installed in it. Everything is connected to a gigabit network and all the cables are Cat5e as far as I can tell.

When I first set up the MSS I was seeing a file transfer speed of over 30MB/s according to Win7. There files were large multi gig movie and TV show files and there related media info packets for XBMC. However now a single day later everything has slow down to less than 10MB/s regardless of how small the file is.

There are three things that have changed since the intial fast speed and the current slow speed.

1.) I added the 2 1.5TB WD Green harddrives.
2.) I turned on folder duplication
3.) I scheduled and preformed a backup of my desktop.

The CPU is running at around 80% durning a transfer and memory is at 30%. My router is a Netgear WNR3500L.

I found a few threads that suggested a scalable solution delivers global deduplication for large data volumes without slowing performance, and I'm going to do that once my current transfer batch is finished.