Hi, Jose.
It is very strange for me, because that is what i see:

I just checked all the jumpers according to the guide and they are all correct.
Can you send a screenshot of your Device Manager window with the connected board?
"But, I’m probably not understanding, are you trying to connect the KITPF0100EPEVBE evaluation board and the PF programmer (KITPFPGMEVME) to the GUI at the same time? This is not supported, and why would you like to do this?"
No, not in same time. I just say that was PF Programmer work fine and problem not in the USB port of PC or KITPFGUI 4.1.