Hi, I think I did not explain it correctly, the problem is not the SS pin for using the SD or any SPI comunication.
What I want to say is if apart your normal working code for SPI/SD by some extra need on your sketch you use those pins (53 or 52) on a pinMode comand those problems show up.
Just do the test or anyone else to understand better, open the "listfiles" example from SD library, them see it working, upload it again and still working ok? Them put on void setup this pinMode(53, OUTPUT); and upload again, stiill working right? Now reupload again the same code and you will get a "No device found on COMx" erro and couldn't upload any further sketch without power out the DUO first, thats it.