Version 2.0.12b for MC 1.9.4 does not save changes to the configuration file when the game is restarted, with the exception of extra leaves.

Same problem here.
MC-1.9.4
Forge-12.17.0.1987
BetterFoliage-2.0.12b

Same with me. I can get the config file to save for one game by regenerating the config file before starting and then changing the settings in mod option on the menu screen, but its really finicky, and it doesn't always work.

Edit:
I absolutely have to delete and regen the config file every time, otherwise when I open a world, I get about 3 fps.

MC-1.9.4
Forge-12.17.0.1976
BetterFoliage-2.0.12b

Fixed in 2.0.13

It is not fixed. Have the latest version and the configurations still do not stay. they revert to default the moment I exit the menu.

I'm having the same issue than UmbraDominus. When I select true to enable reeds in somes specific biomes, each time as I exit the menu it switch to false.
However switching round logs on and off works.