I had the same problem with a 100-chapter book. Since it was my own book, and an alphabetical reference of around 100 subjects, I rethought it and grouped them into about 15 by alphabet, eg, ABC etc. Worked fine.
And it wasn't just with rtf. I run my rtfs through Dreamweaver, as HTML files, to get all the links done. Calibre still didn't seem to like the 100 chapters.
As it turned out, the redesign wasn't a bad thing...the ebook is easier to use in the grouped layout.
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