Thank you for your help,
the problem indeed is the cabling.
We did use the supplied cable, but it was connected through port bracket first (connected to internal MoBo USB 3.0 connector).
When the cable is connected directly to the MoBo backside connector, everything seems to work just fine.
Unfortunately, we have problems using backside connector in our setup (this is a DAQ system in a custom enclosure and there is not enough space for the cable on the back side of MoBo).
We tried replacing the bracket we used with this one: http://www.greenconnection.cn/product-65-en.html (the most expensive in the nearby store) but that also didn't work - same problem (may be a little better).
Could you please provide any recommendations on
1) Cable requirements? Some kind of compliance mark to look for?
2) Cable brands you know works well?
3) Based on your experience, is it possible at all to use the MoBo internal USB 3.0 connector (20 pin header)?
4) Based on your experience, is it possible to use right-angle adapters like http://www.greenconnection.cn/product-122-en.html or is it a waste?
Thank you in advance.
It seems like every manufacturer marks their cables as "high quality", so we would really appreciate some guidance on that.