Upon closer inspection; the failure I received seems to be closer to a problem with USB 3.0 ports in Windows 10. New devices with crystal oscillators still works fine with USB 2.0 ports on Windows 10 computers.
It's worse for OSCCAL though -- if you store the tuning in EEPROM, you can at least unplug and replug the device (I did this on an old Arcade Joystick I built, it's still able to tune itself and store the correct tuning values, but the device will fail the first time on any Windows 10 computer, and then you have to unplug / replug and it will start working). -- It works fine on my Raspberry PI though.
I'm considering putting an inline USB hub between the device and a computer and seeing if that makes it any better... -- I've also considered putting an auto reset -- like if it goes a certain period of time without being polled, it should just reset itself automatically, maybe.