@bmorcos, yes I checked them and checked the customers MSEL too, they
were all good. I cannot make sense of it, so in desperation, I reached out on this forum 
.
And it bothers me that quartus 16.1 says FPPx32 is not supported for that device while
the user manual explicitly mentions this (already a few years):
I searched for a way to see if the rbf file in the SD image is x32 or x16 but there is not much info on that
for fast parallel programming (FPP).
I wanted to see if I could send the customer a FFPx32 file to test but Quartus refuses to.
Still the SD card with the original download Atlas Soc v1.1 works with both boards.
Putting my rbf + .scr + .dtb file on my card works with my board (MSEL =x16)
and not with the customers (and brandnew board, MSEL = x16).