Thanks Mario! It helped with the OpenGL issue.
I still have a problem with XOrgConf. Although I can create an config file and select it without any error message on matlab, it doesn’t apply it after logout/login - even after restart. It is a similar issue with this: AMD graphics card - #2 by mariokleiner
I ran sudo dpkg-reconfigure matlab-support on terminal and it changed only GCC library names. uname -r reports 6.5.0-14-generic. There is no PTB output about XOrgConf. Do you have further suggestions?