Sometimes when changing settings in preferences, GtkRadiant will not save them. This seems to happen most when editing preferences after launching the program for the first time. It also seems to sometimes happen when changing colour shemes, it will change them for the current session but then reset after restarting Radiant.
You can see this bug in cityy's video and I've come across this myself:
I've had the same problem
What's the best way to reproduce this?
See the YouTube video posted above. In cityy's tutorial, follow his steps at the 3 minute mark with a new install of GtkRadiant.