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I have gotten around this problem - there are many ways on how to solve this problem, but since I've started this question, I've sent you the file. No matter how I try, I cannot reproduce it with any other file.
There are two reasons why I started using Sigil. One is to fix the font problem with Kobo device, and the second one is that calibre doesn't build a proper TOC even when you try to set proper headers in RFT file (at least it didn't work for me). So I would go, edit the epub file with Sigil, and set the Part/Chapter structure properly, which recreates TOC. Don't know why chapter do not work well (for me) with calibre and RTF files, I tried Atlantis and it does an excellent job.
In the end, I think Sigil is going to be an excellent tool, once it reaches higher version. And I'm happy that I can use it under linux. The only problem is that it is a bit slow.
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