Can you confirm whether the two boards are enumerating as USB 3.0?
Load USB Bulk Source Sink Example firmware and check whether it is coming up as USB3.0 device either in control center and streamer?
What about connecting the two boards to USB 3.0 port of Win 7 PC? Is USB 3.0 enumeration fine?
Yes, its enumerating as USB3.0 and when I use 2.0 cable the problem did appear.
We tried Source Sink and its USB3.0 device
We didn't have WIN7 PC now, will tired it later
Can you capture the USB Trace either using hardware Analyzer and Software analyzer and compare where it goes wrong in the failure boards?
You share the difference between two traces here for the review.
This will help in understanding the issue.