I would think it might have something to do with what exactly the replacements in question contain. Hard to tell without knowing what content this was exactly, but if one was a texture override and the other one maybe had custom descriptions as well, the latter would require overriding the CASP in addition to the texture -- perhaps that is what makes the game flag it as "custom".
Maybe @SimGuruEugi can give us some more detail on what exactly makes a thing be classified as "Modded"? Particularly in the light of the current situation with Offline Mode (where one cannot access these items anymore) =/
