I have noticed, One of my mining areas (sand on surface only) I set it to dig one tile down below ground level. Then I change it later. The mod then changes it on the fly on its own and messes up the entire area below ground. I suspect it is a conflict with another mod. I am unable to identify which mod.

Are you using leveling designations to dig and do you have farmland preparation activated in ATD? If so, ATD will interpret your leveling designations as an order to prepare farmland, which would start by lowering your set designation by one level, waiting for it to be dug, then later fill it in with soil materials. The process can be aborted at any time by unchecking Automate Farmland Preparation in the tower.

I would also recommend to update to the latest version of ATD, which will persist the Automate Farmland Preparation setting in the vanilla save file.

Farmland preparation has turned on by itself. It looks like a feature, which should be off by default.

I'm not really sure why it was on in one mining tower and off in the rest. I don't recall clicking that option.

Latest version has proper persistence of the Farming Automation setting. I would recommend upgrading to the latest version and report back if you still have issues with Farming Automation turning on or off by itself.

Looks like it's working now. My theory is that farmland got checked at some point without me noticing prior to upgrading and once upgraded, the setting was kept. Regardless of what precisely happened, it seems to be working now, which is the most important part.