I'm also having this issue. I'm not sure it is related, but on both computers where I've had this issue I'm also suffering from https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833930
I've tried to reproduce both issues in a clean VM, first by installing jessie, apt installing xorg+fluxbox+kicad+gitk, dist-upgrading to stretch and rebooting and then by installing jessie, dist-upgrading to stretch, rebooting and then apt installing xorg+fluxbox+kicad+gitk. In both cases, I couldn't reproduce neither issue. I did then try to uninstall libx11-6 and all its dependencies and then reinstall everything on one computer, as that may have worked for #833930, but it wasn't enough and on that computer I still have both problems. -- Elena ``of Valhalla''