Does "preferences" get saved in Linux?
In Windows there is no problem to change the color for (i.e.) free points, then save the preferences and when we open again Geogebra, new points are red. You can even find the files defaults.xml and prefs.xml if you want to manually edit them.
However, I'm trying to do the same in Linux (Ubuntu 17.04, Geogebra 5 from the today deb in the web) and preferences are not saved. If I close and I open Geogebra, styles are default ones. And, as consequence, -xml files do not exist. Running Geogebra as su does not fix this issue.