Turned out that they were having problem with USB 3 ports. When plugged into USB 2 ports, they worked fine.
This (and the other anecdotes above) sound very similar to what I've heard.
The key thing to note here is that most HID devices - keyboards, mice, joysticks - are actually USB 1.1 devices, and USB 2.0
compatible; they only transfer data at low speed (LS, 1.5 Mbit/s) or full speed (FS, 12 Mbit/s), and not at USB 2.0 high speed (HS, 480 Mbit/s). It is exactly the low/full speed devices, 1.5 Mbit/s or 12 Mbit/s, that some USB 3.x host ports and hubs have issues with. (And often they can be worked around by adding an USB 2.0 hub in between.)
I am not an USB expert, and know very little about the actual hardware implementations, but it seems to me there are some (common?) USB 3.0 chips that do have issues with USB 1.1 (or USB 2.0 LS/FS) devices without help from a software driver running on the host OS. Or perhaps they need some specific hardware bootup sequence that some BIOSes don't get exactly right. Or perhaps the chips' datasheets have a note that a certain resistor or capacitor has to be present for initial bootup USB 1.1 compatibility, and those are omitted from some implementations because the software driver "already does it"; cost-cutting.
Because of this, I do recommend using an USB 2.0 host port and hubs dedicated for HID (and USB 2.0) devices, separate from the USB 3.0 ones.
If you don't have enough ports, then splitting off the HID (and USB 2.0) devices from the USB 3 "trunk" using an explicitly USB 2.0 hub (as opposed to USB 3), may also work. (That is, it has worked for those having issues with USB 1.1/USB 2.0 LS/FS native-USB microcontrollers; I myself have not had any issues with this.)
When I am working on a microcontroller circuit connected to my computer and also externally powered, I use a cheap ADuM3160/4160 USB isolator – LS/FS only; selectable via switch, so only 1.5Mbit/s or 12Mbit/s, no 480Mbit/s support! – from fleabay, followed by a powered USB hub (one using an isolated switchmode supply, so I can "ground" it to whatever ground potential I choose). This protects the host computer from my own idiocy (like shorting the USB bus accidentally, or even backfeeding a higher voltage). These cheap USB isolators all use the recommended schematic shown in the ADuM datasheet, only differing in the DC-DC converter they use which in this particular case is basically irrelevant and can even be removed since the downstream USB hub will provide the (isolated) power; but, if you want a good one, the
Olimex USB-ISO is quite nice in my opinion.
That kind of "isolated slow USB branch" can be useful for other situations too, for example when fixing/checking suspicious USB devices.