What exactly do you mean by having "dwc off"? In all of these tests you need to have your rPi running and connected. If you did not that would explain why G28 was not do anything when you typed it from putty. You can't use the SBC version of RRF without having the rPi/DSF connected.
It is getting pretty late here, so I've got to go.
You should probably set the option in the putty terminal settings:
Implicit CR in every LF
makes the output easier to read.
I'd still like to see the directory listing of your /opt/dsf/sd/sys directory.
Please reboot your LPC board. Make sure that DWC is connected and then connect using putty over USB (keep the rPi on and DWC running) then enter:
M111 P3 S1
M111 P16 S1
and post the output.