Ok, I found the problem, but I don't understand how it can be a problem. After fixing it, I wanted to switch around my buildings again. I started by adding the law bonus to the walls again. Tested it, worked fine.

Then, I wanted to change who can build the various roads. Basically, I like shifting everyone up, so those that cap at making paved roads can build up to highways and everyone can build paved roads. Not realistic, but I just have more fun when I can make better roads as barbarians/easterners.

Anyway, I had done this on a vanilla install before with no problems, just cut and paste the people that can build paved roads onto highways and the people that can build roads onto paved roads. After doing this and starting up my cities have no base farming values.

So, I recoded it back to the way it was, and the cities have a base farming value again.

Guess I'll just have to deal with the standard roads, but I still don't understand how that happened to begin with.