I have aslo experienced some similar Wrapper related issues:
When exiting KOID with the "Menu" button (and not with the "Exit" option) and changing the Wrapper settings and re-entering KODI the change made with Wrapper doesn't have effect. It happed with me like 2 times, and it's really dull, while quitting KODI (or just lets say: minimize) with the "Menu" button way is a much more practical and casual way to navigate confortably (specially with the stock remote, whit which you're unable to select "Exit" on the bottom of KODI's GUI, unless you push "Back" button a several times, till it gets beack to the main KODI menu.)
The only solution to this, is run the "Cleaner" on the main Android screen, which will reset KODI, but it isn't a very viable way at all.
But even independently from the issue above, it would be great if it would be solved on the default remote, to be able to choose the proper "Exit" function in KODI, even when we're deep in it's file browser, etc. menus struckture...