capped at exactly 10mbit for LAN but internet is fine at 40mbit?

How is it possible that computer to computer transfers are exactly 10mbit/sec but my internet connection is working fine at 40mbits with the same computers and network adapters? One computer is asking me to activate because I put the CPU back at stock from an overclock. That couldn't be it, right?

I have two Windows 7 computers and a linux NAS server, all gigabit, and each device on the network is connected with only one network adapter. The system was working flawlessly with gigabit speeds for a year, and all I did was replace two motherboards.

By disabling/reenabling the network adapater in windows or restarting the router, I can sometimes get the LAN speed to behave like real gigabit and do sustained 800-900 mbit transfers, but it soon gets eratic and sometimes pauses for a few seconds.

I can eclipse 10mbit/sec with my internet connection with both computers 100% of the time, but for some reason computer->computer and nas->computer transfers are capped at 10mbit/sec most of the time.

edit: I may have fixed it by resetting everything on the network. I was pretty sure I already did that, though. Very strange.