I'm not running Ubuntu anymore, but I can confirm that this is a problem
in Debian Stretch (and was an issue in Debian Jessie). I see similar
behavior for keyboard rates set via `xset r rate`. Plugging in the USB
keyboard resets the keyboard settings. Suspending while a USB keyboard
is plugged in also resets the keyboard settings, though suspending
without a USB keyboard attached doesn't. I suspect that whatever logic
executes on plugging in the keyboard is also run on resume.

For anyone looking for a workaround for mapping caps lock to escape,
setting `XKBOPTIONS="caps:escape"` in `/etc/default/keyboard` (and
rebooting) will do that reliably. That should work for anything that can
be configured via `XKBOPTIONS`. As for the rate issue, I don't yet have
a good workaround. I suspect a udev rule might do what I need, but
that's also clearly a hack, so it would be nice to have a fix for this.

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https://bugs.launchpad.net/bugs/287215

Title:
  xmodmap settings not getting honored when keyboard devices are
  hotplugged

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