Huh, that did the trick. Thanks!

Removed the old installation, fresh new factorio 0.13 unzip. Can't load old maps, can't load new maps. Text below:

factorio@mindsrv:/opt/factorio$ ./bin/x64/factorio --create ./TestMap.zip
0.000 2016-06-28 00:10:54; Factorio 0.13.0 (Build 22782, linux64, headless)
0.049 Operating system: Linux ...