I've also been having the "plants suddenly perfect" issue, though they do generally go back to their actual level, but at the same time most of my plants are at magnificent and I know I haven't evolved all of them that many times.
I also have something that's sort of like resetting, but also different? Every time I harvest, my basil and parsley plants appear to just be a small leaf on the ground. Hovering still gives all the normal options for a plant in the state they should be at (mature), they just look like leaves. When it hits 5 am and the plants all switch to harvestable, they're back to looking normal, until they're harvested again. It was doing this both in my prior-to-EL game (where they had already been planted for a long time and harvested many times without this happening) and in my new game, where new ones were planted and grew fine until they were harvested, then they were leaves until it was time to harvest again.