Do the modified epubs pass epubcheck? (a web-based version is here
http://threepress.org/document/epub-validate/
if you don't have it on your computer.)
Otherwise, maybe it's not the chapter headers but the "invisible hand" of HTML tidy, which is built into Sigil, and which occasionally, silently, modifies the HTML code in an unhelpful way. To test, you could try loading a "good" epub into sigil, make only some insignificant change in the text, and save it to another name. See if it still loads.
If none of the above offers any clue, you may want to ask in the BeBook forum on this site.
https://www.mobileread.com/forums/forumdisplay.php?f=216