Originally Posted by Jellby
Try changing the options in calibre, maybe its automatic structure detection is causing the troubles. If you are starting with a well-structured ePUB, I don't think you need id anyway, try to disable it.
I figured it out thanks to your excellent advice again. In the detect chapters there was a section that had specific words to take out. And low and behold part is in the regular expression (i think that is what you would call it). I took it out and im good to go. Thanks again.