Not intermittent, but absolutely repeatable.
When installed reader is seen and works OK, power light on.
Next re-boot, power light on during POST, goes off when Windows starts up and card reader can't be seen.
On further re-boots, power light never comes on and reader never seen again.
If disconnected and run through a boot cycle back to square one.
What is the time span between reboots.. and does the time span affect this cycle? It sounds like the power supply isn't sitting long enough to completely drain it's caps and they're acting like a backup battery of sorts. Pulling the connect interrupts this "battery" allowing the cycle to repeat. Now.. to figure out what this is telling us.
Which means the reader is supplying some signal to the motherboard which isn't allowing it to be seen. This leads me back to a possible BIOS settings and away from a Windows program. The BIOS and booting sequences are happening before Windows even boots..
It could be an incompatibility with the motherboard.. actually it obviously is. But why? BIOS setting, BIOS needs to be updated, or MB design will never be compatible..
I'd start with making sure the BIOS is updated to it's latest version. If that doesn't fix it then consider a beta version if there is one.
Next would be to contact Gigabyte.. but their replies can take weeks and their form is almost comical in the amount of information they want just to let you ask a question. Still.. this is the choice.
OR/andor/Finally.. Replace the card reader. It's $30.. the MB is a lot more. The one I showed you worked fine for me.
If you had a high end multimeter and the right type of probes we could measure the logic states at the connector and find out which one is being left hot.. but this bit of knowledge wouldn't change your subsequent steps.
This issue seems specific to the Intel header on the motherboard, not the rear sockets on the VIA controller.The first reader was originally installed within a day or two of commissioning the system. It's just taken a while to define the problem. Not sure what doing this would tell me that I don't already know. With the OS on a SSD reboots are pretty fast anyway.
I'm assuming you've checked for the latest drivers for the USB3 controllers? If I'm right above this 'shouldn't' make a difference but it's still a good practice.
When I connect these I either go through the back panel like in that link I posted.. or I use the 20 pin adapter (also in the link) to to connect to the MB connector.. and no issues with the Koutech.
If it works right on one USB3 controller and not the other.. this means it's almost for sure a BIOS/motherboard issue WITH that specific reader. Gigabytle will never know to fix it if it's only the one reader and not all of them.. especially if people don't take the time to fill out their question forms. You've tried their forums? Often I'll find the problem and solution in the same thread..
I can't tell you exactly what John in thinking though I have a guess.. but I'm sure he knows. His hardware logic rarely is off.
