The conflict is in Data\Flags. For example in the 'Vivec, Telvanni Plaza', Window Glow has a value of 1D and my plugin has a value of 05 (which is the same as morrowind.esm).
If i remove the 2 additional flags in Window Glow with EE, it doesn't seem to have an effect.
So my question is, why does Window Glow change the flags in a lot of cells? Is it necessary? What does these changes do?