Originally Posted by bookraft
I used calibre to split the file before a designated paragraph style rather than a character style and that also didn't help.
On the other hand, I've just used Sigil to do the same thing, inserting a chapter break before each paragraph, and this works.
So it seems that calibre isn't working well with embedded anchors for some reason.
You brought up some fair questions. As JSWolf says there are many ways to skin a cat. Calibre works great on h1, h2, h3 tags etc... to create proper external TOC for ePubs. It also seems based on your info that it does great with functionally splitting things the way you like but ePubcheck left you wanting.
Calibre is not a ePub creation / publishing tool. It is a ebook management tool and it also does a great job of converting books from one format to another format. This conversion process promises to create a readable book for our use.
Most likely further questions about refining your books to pass flightcrew or ePubcheck should be asked in the ePub forum
That said, if you think something you run into in the future is a bug or you need help doing or understanding something don't hesitate to bring it up in this forum. You can also request enhancements or report bugs through calibre's site, learn how here
Good Luck with your projects.