If I hook up my USB via a cheap pocket hub to my notebook the error rate drops right off to < 1% (short test so far). So there's a quick fix for those wanting to see if the USB noise is causing the error issues.
My guess is that the hub has correct EMI filtering beads on it's connections and acts as the filter we need.
Looking at this now - EMI2121
http://www.onsemi.com/pub_link/Collateral/EMI2121MT-D.PDFMore report.
Now I have all the 16 chips mounted on the board running at 256MHZ. The HW error rate is higher than before at ~ 30%.
If I lower the freq to 128MHz, the HW error rate drops to less than 10%.
From the chip statistics, I can see that some time 15 chips are working but at most time 13 chips.
I just grabbed a 4 port USB hub the same as this
http://www.canadacomputers.com/product_info.php?cPath=48_794_259&item_id=038391but it doesn't help the HW.
I think the key is the report signal clock generation circuit or the capacitor value (I am using 30pF).
I don't know why your clock signal is so sharp. Are you using 74AUP1G02 NOR gate?
I've added the inverters on mine. Immediately before PIC one each on clk and data.
Same as clock buffer - NL27WZ14.
But even before that I was getting much better error rates. I consider 3-5% to be bad enough and on my notebook without hub that's what I get. The hub doesn't do as well as the RaspPi though. It consistently gets <1%.
The new board revision has both Dual NOR gate and inverters, I've completed it now except for adding beads on the USB signals. I worked all night on the ferrite beads on the ASICs, moving the PIC to make room for the beads, and generally improving the routing here or there.