What is the directory structure inside the ePUB? Do you have a <base> tag or similar? Can we see a full (non-)working example?
It should work if you have a structure like this:
Code:
mimetype
META-INF
container.xml
OEBPS
content.opf
TableOfContents.xhtml
Chapter-1.xhtml
Chapter-2.xhtml
...
and, inside "TableOfContents.xhtml" there's a link like:
Code:
<a href="Chapter-1.xhtml">Chapter One</a>
that's because "TableOfContents.xhtml" and "Chapter-1.xhtml" are in the same directory. By the way, "TableOfContents.xhtml" is included in the OPF file, right?