Hi Pierre
120 degree is the phase difference between two phases and not between V and I of a particular phase, right? PF register reading is computed by dividing "abs (active power)" by "apparent power". The sign of PF will be equal to the sign of fundamental reactive power. So, kindly check if the PF values make sense based on this description. ANGLEx registers display the angle measurement. ANGLESEL bits in the COMPMODE register can be used to determine which angle is represented in the ANGLEx register. This you can configure to display the angle between voltage/current signals of two phases. Refer to page 32 of Rev.A datasheet for more details on this.
You should also double-check the board's jumper settings (as I think what you are doing right now isn't entirely correct) and how you connect the phases and neutral to the board in both configurations. Can you let me know at which terminals you provide the signals to the evaluation board? Refer to figures 6 and 7 on user guide to see how the connection needs to be done and how to set the jumpers correctly. In figure 7, the representation of phase coils and load is incorrect (it should be in delta config), but otherwise the connections are represented correctly. Phase B is used as the reference in delta mode and so no input is connected to the Phase B voltage and current channels on evaluation board. So, ground the inputs for Phase B. (connect IB like IN in figure 7).
Regards
hmani