So further testing, my Second unit came in and it experiences the same issue.
Tried unplugging fans, one by one, then all off, none of this affected the speed of the fans.. CPU temp is in the 30C's with fans on.
Plugged in 3x 80mm PWM fans that I had. They ramp up and down depending on CPU temp as expected, 4th fan (delta) still stays at 6000 rpm. Moved the delta around, same results.
There are some jumpers on the backplane/fan connection, but they're not labeled as to what they do. I have yet to find a motherboard manual that goes in depth on the jumpers of the motherboard or backplane.
I've gone through 3 firmware revisions of both Bios and BMC, all exhibit this. You can't use IPMITOOL or IPMICFG to reset the BMC, it gives a Code 1h error.
Fan speed issue is a known problem on some Supermicro boards, the fix is to reset the BMC, this does not work for us.
ASPEED makes the BMC. You can find some utilities here
Driver Downloads:ASPEED 信驊科技
The system test utility didn't really do much for me, the readme sucks. It's more for testing connectivity and video display.
At this point I'm just going to replace all the fans. No point wasting time on this.