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?
Update:
The error rate lowers to ~5% @256MHz after I moved from a desktop to a laptop.