Actually when I read this thread I think the following things...
1) What hardware is FreeNAS running, maybe it's a 4GB RAM issue or the drive is over 90% full? No one has asked this and gone on face value that it actually ran fine at one time. Never take things at face value, always confirm it. It will keep folks from spinning their wheels and that is why we put that into our basic forum rules. Yes I may sound like a prick saying these things but trying to troubleshoot a problem remotely without all the facts is extremely difficult and I'm not saying them to hurt anyone's feelings but the problem will not get solved as quickly for the OP without these kinds of details to at a minimum rule out some possible issues.
2) The Windoze computer could be the cause of the iperf slowdown, I've seen it before and you know we will see it again. The best solution here is to get a bootable OS like Knoppix or FreeBSD Live and run iperf from there, this takes out all those Windoze issues. You can use your Windows machine without harming it.
When doing future throughput testing, directly connect your FreeNAS computer to your testing computer, nothing but a single Ethernet cable. All Gbit Ethernet ports should be auto switching so they can handle any Ethernet cable, they do not need a crossover cable.
Good luck troubleshooting this, I hope you get it resolved soon because no on like a slow transfer rate.
Just my two cents...