wil do some more testing after dinner

A USB cable has four wires: "ground", "data one/+/a/forth", "data two/-/b/back" and "+5V vcc".
Designations vary sometimes, like in that link I included earlier, but usually, it's obvious enough which is which.
Those terms describe what each cable does.
Colors, however, do not.
So, whoever published that sorry excuse for a documentation should be banned from the tech business for life.
Sadly, the market itself does not take care of such things.

But, anyway, it very much seems that the producer of that card reader simply assumes there's only one kind of USB port around, the first "missing leg" type in that link.
So, chances are you got that right as it is.

(To test anyway, pull one of the plugs on the mobo. If the frontside USB keeps working, rotate it 180 degrees, see what happens, but at your own risk. Don't think it will damage anything, but that's what documentation is for.
If the front USB does not work with that plug pulled, then that's his plug - that one is a mere passive extension of the USB header, same as any slot bracket for the back. Leave it, it works. Test the other one.)

The 9- or 10-pin USB headers on the mobo are two USB ports each, side by side. Those front card readers tend to have an extra USB port for that simple reason - to make use of both, while the card reader will only ever need one.

That being said, giving eight different colors to two sets of cables with the exact same function, instead of, say, twice "black, green, white, red", like sane people, is patently idiotic.
Also, if they don't provide a pin out and assume that one single, fool proof (coded) type of USB header - why on god's earth would they not just provide the solid "5 x 2" plug with the missing hole that goes with it, without any questions needed?!?

Never ever buy that brand again and consider burning down the place you got it from, please.

Anyway - it does get "recognized" as new hardware, hence the message in windows. It just doesn't work. Needs the correct drivers, I very much assume.
At which point I'll have to leave you to people here who do windows. Probably would be running with a mainstream Linux distro right way.
Good luck! 😀