I have re-done the conversion from scratch so all files are clean.
I have had to ZIP up the ODT to upload it.
The problem is as described in the original post and the affected file within the EPUB is index_split_033.xhtml.
I am viewing the EPUB with SIGIL, however I have now exploded the book with Calibre and examined the offending files with Notepad and it appears that on opening SIGIL is changing all files except ..._033. In the directly converted EPUB the stylesheets are in the same folder as the text files, SIGIL must be changing the structure on loading to put the css files in a Styles folder (and creating other folders) and not doing a complete job.
If this is the case then the problem is not with the Calibre conversion but it appears unwise to use the "Open with Sigil" option in Calibre to make changes to the EPUB without being aware of possible side-effects such as this.
For completeness - I have just downloaded SIGIL 0.71 and that does not create the problem I had previously so my comment on not using SIGIL is only applicable if using 0.70
Last edited by BobC; 03-18-2013 at 08:43 AM.
Reason: Added reference to SIGIL 0.71