May have possibly found it, was looking at https://github.com/bsdperimeter/pfsense, and found hw.usb.no_pf="1" was added two days ago to the loader.conf. (http://redmine.pfsense.org/issues/2306) Even though this refers to disabling the USB buss from showing as a network interface. I did think this could possibly be having an effect, I added a system tunable and set hw.usb.no_pf with a value of 0. After a reboot, below is the output from iperf, internet performance running a test on www.speedtest.net appears to be back up to normal.
8] local 192.168.5.3 port 60103 connected with 192.168.5.1 port 5001
[ ID] Interval Transfer Bandwidth
[ 8] 0.0- 1.0 sec 9.00 MBytes 75.5 Mbits/sec
[ 8] 1.0- 2.0 sec 7.00 MBytes 58.7 Mbits/sec
[ 8] 2.0- 3.0 sec 5.75 MBytes 48.2 Mbits/sec
[ 8] 3.0- 4.0 sec 8.75 MBytes 73.4 Mbits/sec
[ 8] 4.0- 5.0 sec 6.88 MBytes 57.7 Mbits/sec
[ 8] 5.0- 6.0 sec 8.88 MBytes 74.4 Mbits/sec
[ 8] 6.0- 7.0 sec 7.00 MBytes 58.7 Mbits/sec
[ 8] 7.0- 8.0 sec 7.75 MBytes 65.0 Mbits/sec
[ 8] 8.0- 9.0 sec 9.50 MBytes 79.7 Mbits/sec
[ 8] 9.0-10.0 sec 3.88 MBytes 32.5 Mbits/sec
[ 8] 0.0-10.0 sec 74.6 MBytes 62.5 Mbits/sec
It's possible though that the problem doesn't show up for a little while, so I will redo tests later today and see if the problems back or if this did indeed resolve the problem.