My first thought, is that they may be nonstandard plant containers from some other mod. Alternatively some other mod may be (likely unintentionally) changing these plants back to normal.
Try this: Bring up the console (~ key), click one of the offending plants and type ORI. If the File is not Morrowind.esm, then there's a good chance you've found the mod causing this. Next check the "Reference" (AKA the Object ID), if this looks unusual (i.e. starts with anything other than "flora_") then it's a whole new object, and compatibility patch would be required to make it work the Graphic Herbalism. If it's a standard ID, then the simplest solution is to change the load order so Graphic Herbalism loads after whatever mod is interfering. This could potentially cause problems with that mod, but more likely I think the plants were changed by accident, or changed in some trivial way, like the number of ingredients, so it won't really matter.