I was able to pin point the exact mod that was conflicting with yours. XSkills 0.4.9 by Xandu
I am not sure how to proceed. If I should be talking to you, or if I need to discuss this with Xandu for a possible fix. That is if it can be solved. I have no idea on the complexity of such things, and that is why I am glad to have dedicated people like you do things I can't. To elaborate when XSkills is enabled. The farm blocks disappear as if your mod was not enabled. Even when the nutrients are at there full capacity. When I turn XSkills off, I get the soil back as intended by your mod.