So THAT is what's causing it!
I was getting really annoyed with all the new stuff going on all of the sudden. The stuck at work bug, the garbage collector acting as if they own the place (even happily sitting behind my computer) and most of all the super-annoying part where any visitor to my lot thinks it would be fun to harvest all my plants before I have a chance to (even before they ring the door bell). Maxis is really punishing us with those NAP's.
And then I noticed that I had not needed to evolve any of my plants, they just went all the way up to Perfect at super speed without any interference from me. I was okay with that. But the it turned out that every time I traveled somewhere and came back, the footprint went back to Neutral and the plants all went back to various states of Magnificent. Resulting in Magnificent harvests which I then have to sort fro the Perfect ones since that is the part the new inventory system still can't do (selecting only non-perfect harvestables in my inventory, or the other way around). A few days later the Footprint is back to Green and all plants are Perfect again.
Other things that happen upon returning from travel is that the bug houses are suddenly less healthy and the night light goes off (resulting in monsters under beds).
The only bug I'd call an exploit is that half the time when I rummage in the thrash can, it generates a new thrash pile on the ground, resulting in a constant ability to rummage and search piles. Can easily go 20 times in a row.
I think it's time to break open S4S again. I've never had it this bad.
My lot is an off-the-grid on the small lot on Windenburg island by the way.
@crinrict Is it really still unsure at this point? I think we can safely conclude the issue is linked to the Eco Footprint changing. A badly calibrated feature from the looks of it. Mixed in with a few bugs for flavor.