So you don't want to just delete the dead plants in buy mode?
A couple of times, I've had a sim refuse to weed a plant, and an MC reset fixed it. (It might have been a reset of the weeds, not the plant, but it worked one way or the other.) So if you have mods, maybe the same thing will help.
Otherwise, maybe a clean game folder? You never mentioned clearing the cache files, but a new folder would accomplish the same thing, and also clean up some other stuff that might be causing problems. After you move over your existing saves and other content, the plants might decide to be a bit more cooperative.
