Just to be sure: Yes, it says after having added a texture folder that the texture was y X z X 16 - but it isn't. What we have here is nothing but a Conitec-typical inconsistence in GUI creation... they simply implemented the same infobox no matter whether the texture is inside a WAD or a folder.
So, if you haven't - give it a try. Does the problem definitely occur with texture folders instead of WADs?

Cheers