It seems the values for these variables are user based.

Then if you run the command "gconftool --get
/system/http_proxy/use_http_proxy" with a user that is not the proper
one, you get that error.

In /etc/cron.daily/apt you have:
admin_user=$(getent group admin|cut -d: -f4|cut -d, -f1)
and:
use=$(sudo -u "$admin_user" gconftool --get /system/http_proxy/use_http_proxy)

This mean the script uses the first user in the group admin, that in
this case is my login user.

I added the root user in the group admin, look like it's fixed now. Had to 
check also if variables were set for user root though, they usually are.
Don't know why a cron job (running as root), would sudo quering the conf table 
of the the first admin user for the info on the proxy. Looks like a workaround 
or something unclean, even more for a server install.

This procedure is used also in other cron scripts.

-- 
apt cron.daily script doesn't check value-existence
https://bugs.launchpad.net/bugs/223502
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