Roxterm seems to be at fault here. It has two bugs in it's installation scripts: 1. It writes directly to /home/user directory (it also assumes that user's username is user) 2. It creates /home/user/.config/roxterm.sourceforge.net directory, but it assumes that /home/user/.config directory exists because it only chown's /home/user/.config/roxterm.sourceforge.net directory to user. So if .config directory didn't exist it is owned by root after installing roxterm