In the latest release, I have Better with Wheat enabled, but the behavior is still default vanilla minecraft behavior. There's no recipe for hay, wheat is still ground into flour, etc.

In the config under the betterwithwheat part of the config put the:
B:Enabled= true
This will enable the betterwithwheat part of the mod.
By default this is on false and thus off.

As I said, I have all the relevant sections in the config file enabled.

    betterwithwheat {
        # Haybales require hay instead of wheat.
        B:ChangeHayBales=true

        # Changes textures of Wheat and Wheat Seeds.
        B:ChangeTextures=true

        # Carrots and Potatoes cannot be instantly harvested, and instead have a breaktime and a preferred tool (hoe)
        B:DigUpCrops=true
        B:Enabled=false

        # Instead of milling wheat into flour, wheat seeds must be milled instead.
        B:MillGrain=true

        # Wheat, when harvested, will drop wheat and hay instead.
        B:ReplaceWheatDrops=true

        # Wheat can be threshed into seeds using shovels.
        B:ThreshWheat=true

        # Wheat can be threshed into seeds using a millstone.
        B:ThreshWheatMill=true

B:Enabled=true
it's false in your config

The one in the carrots and potatoes section?

yes, it's only collapsed like that because it doesn't have a description, I've added a description but not pushed a new version yet unfortunately.

Ah, okay. I thought that was for enabling the carrots and potatoes modification. Thanks!

I wasn't very clear i guess, but i am glad you found it now.
I actually ran into the same issue earlier and remembered i used to have to change one config value that was less obvious last time.

this is resolved i think