Um, 4PM yesterday
davidfor bumped the version number from 3.1.5 to 3.2.1, which is the first kobo driver fwversion update in 2 months. Are you sure it (device) is fw version 3.1.1?
It should be all right, though, as the comment for the commit says it was already compatible, and only the version number needs to change.
No idea why Kobo wouldn't eject if no programs were still accessing it, maybe calibre wasn't fully closed down? You can try ejecting from the dropdown under "Device" so calibre will quit its connection to the Kobo, which may or may not solve it.