check the documentation regardng checking "as full body morph" feature.

You may try giving the skirt another run thru the program, selecting all instances of the morph in all body parts affected and applying to skirt differently and saving out with a diff name to test against your first conversion.

Good suggestion with WW esther, I havent any experience with that for applying clothes to custom morph chars yet but there seems to be a LOT of happy excited users of this program so im sure Phil has come thru yet again :)