I have some speculation on what might be going on, but I'm not sure.
It seems like it's all of your Agricultural mods causing this in different circumstances, due to how the Agricultural Tower visualisation seems to work. From what I can tell, the tower doesn't care about WHAT plant you're going to be planting, just that ANY plant can go there. In cases where soils for multiple mutually-exclusive plants overlap within the same Agricultural Tower sector, the tower's just "Yup! All plantable soil. No need to highlight." My guess is that Wube hard-coded this behaviour with the expectation of plantable biomes never overlapping like that. With your mod adding more plantable soils with potential overlaps, it's causing aberrant behaviour.
I had a look through the API, but I couldn't find anything which explicitly controlled visualisation. Near as I could tell, "plantable soils" is controlled by the autoplace behaviour of the plant entities themselves. If you can selectively disable visualisation, though, then you know something I don't :) How is that handled, in case I decide to do my own farming thing (such as farming fish)?
Also, thanks for having a look.