@slowsmile: I believe that I've found cause of the Linux problem. Linux is case-sensitive and the actual file names and the manifest entries don't match. E.g., the epub contains
Chapter_
Three.xhtml, but the manifest lists
chapter_
three.xhtml.
I intercepted the temporary epub and attached it to this post. The epub contains:
Code:
Chapter_One.xhtml
Chapter_Three.xhtml
Chapter_Two.xhtml
title.xhtml
contents.xhtml
cover.xhtml
however the opf manifest lists:
Code:
<item id="cover" href="Text/cover.xhtml" media-type="application/xhtml+xml" />
<item id="contents" href="Text/contents.xhtml" media-type="application/xhtml+xml" />
<item id="title" href="Text/title.xhtml" media-type="application/xhtml+xml" />
<item id="body1" href="Text/chapter_one.xhtml" media-type="application/xhtml+xml" />
<item id="body2" href="Text/chapter_two.xhtml" media-type="application/xhtml+xml" />
<item id="body3" href="Text/chapter_three.xhtml" media-type="application/xhtml+xml" />
When you import the epub into Sigil with a plugin (or oṕen it directly) all files that can't be found will be silently skipped. To fix this issue, you'll have to make sure that the manifest entries exactly match the actual file names.