Well, I recently went from DarkUIDarN (in which I had no problems) to regular DarN (in which I do). I did use the OMOD version, and chose specifically NOT to overwrite that file because it had been added by Supreme Magicka, which is why I interpret it as a conflict between them :shrug:
On the DarNUI page in the compatibility section it says this:
Raised Spellmaking Enchantments Limits/Supreme Magicka/L.A.M.E: This funcionality is already part of DarNified UI. The settings are in enchantmentsetting_config.xml.
So, it looks like you are intended to install the DarNUI version of that XML file, and then edit DarN's config file to suit the settings of Supreme Magicka.
I'm assuming it's only the enchantment restrictions that are an issue here?