I've had this annoying problem for a while now, where a black rectangular box appears on my Ubuntu desktop, running Cairo Dock. Most of the links I found on Google didn't pinpoint anything useful so I sat down one day and killed off processes manually, one by one, in an effort to locate the source of my problem.
It would appear that the culprit is update-manager. The process was listed as running with an option/switch of --no-focus-on-map. The full process is shown below:
john 14771 1 0 Aug04 ? 00:00:11 /usr/bin/python3 /usr/bin/update-manager --no-update --no-focus-on-map
lsof -p 14771 shows that /usr/bin/python3.4 is involved, but not sure if that information is of any use.
You can't move the box or do anything with it. The most annoying thing is that it is 'Always on top' so you cannot see anything behind it.
Simply issue the following command at the shell: