Hi kbit, thanks for using Ubuntu and thanks for taking the time to file
this bug report! One thing that can sometimes cause differences between
behavior at startup and otherwise is timing. However sometimes the
terminal behaves differently as well. Let's figure out which it is:

First, try copy and pasting the same command into a run box such as
Alt+F2. Does that behave the same as running from the terminal? If not,
it doesn't have to do with startup. If it does behave the same, it might
be a timing issue. Try putting something like "sleep 10 && cairo-clock
-x 1000 -y 200 -w 127 -h 127 -s -t default -o -i -e" (without the
quotes) into a cairoclock.sh file, chmod it a+x, put it in your home
directory and run THAT instead of the command directly. This will wait
10 seconds for everything like compositing to start up, which might
somehow cause an issue.

Let me know if either if these is a fix for you and we can figure out
where the issue exists, thanks!

** Changed in: cairo-clock (Ubuntu)
       Status: New => Incomplete

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Default theme background texture scaled wrong
https://bugs.launchpad.net/bugs/246556
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