One of the discouraging things about Amtrak livery and logos is how ugly they are. However, even if a logo is ugly, there's no reason to change it and confuse people unless the replacement is clearly better. The "four arrows" was nice but undistinguished; the CT is pretty ugly.
The trouble is that bureaucrats have bigger egos than they do esthetic sense. My guess is that someone at Caltrans wanted to make it clearer to the traveling public that most of the subsidy comes from Sacramento.