I've tested without any mods or plugins of any kind and on a new install having gone through my hard drives and deleting any file that was related to skyrim. The issue apprears with or without dawnguard, the high texures and any mods. I also tried and replicated the issue on a completely new character.
The plant problem appears regardless of whether I reset the cell using resetinterior, use a reset timer mod, or reset the cell by waiting outside of it for 30 (10) days.
I tested primarily with the Arch-mage's Quarters. I picked most of the items in the alchemical garden, then left and reset the cell. I also took all the potions next to the alchemy stand. I then saved. The save image shows the garden and potions still back. But when I reload, the garden is always missing the plants I picked. The potions are always repawned. I also tested this with the plants near the Blue Palace in Solitude.
Is anyone else having this issue? It all started because I was tired of my quarters looking dull because I'd picked all the plants. So I downloaded a mod to change the reset times to a day. It seemed to work, but when I loaded the last save the garden was gone again. I think at this point I've tried everything I can think of and the issue doesn't appear on google searches or the list of bugs that I could see. Installing the Unofficial Patch doesn't help.