I have used the proxy settings once. I used the Ubuntu/GNOME tools and then also made the mark for “set the proxy system wide”.
Now I realized I could not do any bittorent or downloading from FTP. http and https worked. I had already disabled the proxy again.
I then did a grep “proxy /etc/*” and found that Ubuntu had written the proxy into /etc/environment. This was not visible for the general user. I only saw that Transmission told be that the port that I wanted to open was closed. But I knew from testing from external that it was indeed open. So somehow Transmission read /etc/environment and ignores all user settings once you have set the proxy systemwide. Removing the entry in /etc/enviroment and logging in again did the job.