I didnt know this, but it looks as if that command sets Vista's tuning of TCP/IP to 'off', in an effort to speed up raw network speed. Check here for more details:
MSFN Forums > Heres why TcpWindowSize does not work in Vista
Although the author doesnt seem to believe in its usefulness. I cant say as I havent tested it.
Transferring from a USB2 drive should not affect network transmission of files as USb2 has a throughput of 480Mbps.
You should see between 30-60MBps IF everything in your network is working properly:
PC -> Cat6 cable -> router gigabit port -> Cat6 cable -> gigabit port on your NAS
You need to check all your lights and connection staus messages throughout your network to ensure everything is talking on a gigabit connection.
If you wanted to take your router out of the equation for testing, you could get a Cat6 crossover cable and connect your PC directly to the NAS and then test throughput.