My understanding of your comment is that you tested KDE and GNOME on two
different machines. That easily explains why one can work and not the
other, ignoring the desktop environment difference.

The difference with ",,," should not be a problem, it simply comes from
the code in the backends that always print thos, even when the fields
are empty. That should not be a problem, and the error seems to happen
before usermod even reads the file.

Now we would need the help from somebody more familiar with usermod's
codebase. Maybe reporting the bug to Debian could be good.

-- 
usermod fails: "cannot lock /etc/passwd"
https://bugs.launchpad.net/bugs/432964
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