nRF52840-PDK and Power Profiler Kit not working properly

Question

Hi, 
 I am trying to use the Power Profiler Kit (PPK) to asses the power consumption on a nRF52840 - PDK. I have not managed to get anything wokring. 
 The exact hardware versions are as follows: 
 
 nRF52840-PDK 
 PCA10056 
 V0.9.0 
 2017.10 
 code for testing: blinky_pca10056 (On standalone power the LEDs flash sequentialy as expected) 
 PPK: 
 PCA63511 
 Rev. 1.0.0 
 2016.27 
 I have followed the quick start guide on both the infocenter and the pdf which they say the same. 
 http://infocenter.nordicsemi.com/pdf/PPK_User_Guide_v2.2.pdf 
 http://infocenter.nordicsemi.com/index.jsp?topic=%2Fcom.nordic.infocenter.nrf52%2Fdita%2Fnrf52%2Fdevelopment%2Fnrf52840_pdk%2Fhw_measure_oscilloscope.html&anchor=hw_measure_oscilloscope 
 and yes I have chopped and pass the beeper on the SB40 solderpad. 
 I am using the nrFConnect (v2.5.0) with the Power Profiler app(v2.0.0). If I connect the nRF52840-PDK alone, it asked to update the debugger firmware. In the moment I connect the PPK, the board is no longer recognised by the PC (usb disconnection) and the U2 IC starts to get hot. 
 Notes 
 - I have also tried on a different nRF52840-PDK(v0.9.0 - 2016.48) to cut SB41 but that did not help. I read this on a devzone post. 
 - There is no indication on how the switches should be set on in the nRF52850-PDK so I left them as in the default positon (SW8 - obvioulsy ON, SW9 - VDD, and SW6 - DEFAULT). The switches on the PPK as indicated on the guide. 
 
 It is the first time I am trying to use the PPK and I have tried everything before asking here so any help will be most welcome.