I think I am closer to isolating cases where search does not work across all text files. If you use a search argument (using CMD-F) that is across multiple lines of source, it often does not work across all files
e.g
<p class="calibre_4">
<img src="\.\./images/line\.jpg" class="calibre_5"/>
</p>
will not search across all files in the current book I am editing.
If you change this to
<p class="calibre_4">\s+<img src="\.\./images/line\.jpg" class="calibre_5"/>\s+</p>
then the search works across all files
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