Bitfury experienced a similar thing.
Yeah, I know
once I have fewer things on my to-do list I think me and him and anybody else interested ought to heckle forums.xilinx.com until they own up to this issue. I have been seeing the very same "center of the fabric drops out first" phenomenon, but until I read about his experiences I had it chalked up to my crappy homemade boards. Now that I'm seeing it on ztex's boards too I am kinda disappointed with X.
Inspector 2211 already mentioned it and it is also hidden in the datasheet ("Simultaneous switching" issue): The internal GND traces of the S6 seem to be a little bit weak.