PCIE SATA controller ASM1062 problems or software

[Nikolay_Po]

I did a continuity test between sbc mounting bolts and hdd case and it is good.

Have you a network analyzer up to GHz range? The noise that can disturb SATA operation is high frequency. And usual continuity testers doesn't work at high frequencies. They are DC usually and can't help gere.

There are mounting posts in the nas case that you screw sbc to. See below youtube video and forward to 1 minute.
https://www.youtube.com/watch?v=_UeeklKo0Og

The case has metal mounting posts. But has the SBC a metal contacts at these posts? Have the case posts an electric contact with SBC ground? 

As i tried with single hard drive and still get the same issues it has to do something with timing for drive to spinup. 
What you listed regarding ground may help with errors during copying of the files but looking at it as none electronics specialist, connector that has 4 pins on pcb close to dc jack feeds the drives with power, yes there is a converter of some type in between to reduce 12v to 5v or 3v but i would think ground should be solid.

I can't say about the timings.
Saying about good contacts you're saying about a DC path. Yes, it is good. But long black wires of DC supply can't forward high frequency energy good enough. Additional contacts are needed. That is why the motherboard in generic PC is screwed by many screws and the mounting holes of PCB are metalized.

Anyway try to place a link between SATA controller board screw and an RJ-45 shield just to check will it change something. Also place SATA cables togeter with power that manner the look like a common single cable.

If nothing above helps, the problem is definitely a software problem