The KFX Output plugin should convert page numbers from an EPUB source. However many EPUBs do not contain real page numbers. Adobe Digital Editions will make up page numbers if none are present in the EPUB being displayed. Perhaps that is happening in your case.
If you feel that an EPUB has page numbers that are not being converted you can post it here for me to look at. (Make sure that you do not post copyrighted text on MobileRead. There is a
ScrambleEbook plugin that can be used to remove text from a book leaving behind the formatting and page numbers.)