USB3.0 ports on backplate vs internal not same ?

I found a strange issue with USB3.0 while the first use of Agestar 3UB301 3.5 hdd box.

SVG4K wrote: I found a strange issue with USB3.0 while the first use of Agestar 3UB301 3.5 hdd box. Mobo currently is ASRock Z170 OC-F, Win 8.1.  The external enclosure is claimed to be USB 3.0 compliant, handles over 3TB disks, and i experienced strange behavior while trying to write/read and found that while being plugged into internal USB3.0 port, its operation is unstable, some interruptions occur thus showing some IO error. But while being plugged into USB2.0 and USB3.0 at backplate everything is okay. And this seems to be a common problem elsewhere, because at their forum i found a hint to connect into external USB's. For more, @ GA-Z170M-D3H-DDR3 mobo i plugged a 4G USB modem into internal USB3.0 and it failed to find network in any band.. Then, i repluggent the cable into another internal connector, and voila.. it works. And it is said other option to deal with it is to disable power management in all USB controllers section (not sure it matters afaik) So it seems that one of internal dual-ports of USB3.0 is somehow wired differently or provided by third-party chip ?

To clarify, the USB 3.0 "internal connector" is the rectangular header on the mother board that the front panel USB 3.0 cable from a PC case is connected to. These connections can be two cables into one connector with a blue connection that plugs into the board.

As said above, the internal (mother board USB 3.0 connections) are Intel USB 3.0 ports. But the difference between them and the USB 3.0 ports on the IO panel is the internal/mother board USB 3.0 connections are behind ASMedia ASM1074 USB Hub chips.

The hub provides two USB 3.0 ports, but connected to only one USB 3.0 connection. The hub shares the single USB 3.0 connection with two USB 3.0 ports. The USB 3.0 connection is multiplexed (switched) between the two ports.

When using USB flash drives in these USB 3.0 ports, the intermittent nature of copying files to and from a flash drive work fine. But apparently, the modem and your external USB to SATA HDD box (is that correct?) requires an uninterrupted connection between the board and these devices. That is not surprising. You said yourself you saw interruptions and related IO errors. That is my theory regarding what is happening.

Why the modem worked in one USB 3.0 port and not the other is strange, unless the other USB 3.0 port was not through a hub. If both were through the same hub, then possibly one USB port is considered primary, and the other secondary? Or the hub chip senses activity and the lack of activity, and only remains locked to the device when is senses activity. If activity is lost from its perspective, the hub then polls (checks) the other USB port for activity.

The power saving features (thanks laptops, and Microsoft and Intel's need to inflict the mobile PC environment onto the desktop  PC environment) may also play a role in this, be sure to disable any such power saving options, in their Device Manager entries, and in the Windows Power Plan, Advanced settings.