I'm assuming something about the internal electronic frequency of USB 3.0 isn't filtered correctly inside the device.
When they were designed 3.0 didn't exist so something probably wasn't accounted for, this is one of the reasons though most MOBOs still have legacy ports.
Still I never got to the bottom of it as now it's working perfectly, it was always one of those things I was curious about researching more in the future.
There is no "USB 3.0" frequency when device operates in 2.0 mode. Even different wires within the port are used. Also IME Logitech unifying receivers work just fine in USB 3.x ports.
When they were designed 3.0 didn't exist
It did exist, unifying receivers are not that old. And even if they did not, and had the problem, they would be redesigned.
https://ir.logitech.com/press-releases/press-release-details/2009/Logitech-Unifying-Receiver-Eliminates-Need-for-Multiple-Wireless-Receivers-for-Keyboards-and-Mice/default.aspx
My K400r came out in 2011, "the first certified USB 3.0 consumer products were announced on 5 January 2010, at the Las Vegas Consumer Electronics Show (CES), including two motherboards by Asus and Gigabyte Technology". Design would of started for my keyboard before 2011 and if you remember back then, 3.0 wasn't ubiquitous.
https://en.wikipedia.org/wiki/USB_3.0Yes, I'm well aware designs for USB specs are being fleshed out years before consumer release, but my point was they were designing a USB 2.0 product and they probably didn't take USB 3.0 into account.
I'm not claiming to know the exact cause, I'm claiming to have experienced the issue and to know a solution.
I was as surprised as you by the results and would love to know the reason why this is the case.
I posted this to try and help some people, lets please be constructive.
I'm happy to answer any questions, if there's something you think it might be that you'd like to test.
Just becuase you haven't encountered the issue doesn't mean it doesn't exist.
I'm not the only one with this issue, many people have encountered it.