I don't think it is the files I'm working with, I can reproduce the behaviour with a very simple epub created from scratch in Sigil.
Using Sigil 0.2.3, Windows XP 32bit.
1. Open Sigil.
2. Select code view and enter "<p>cat</p>" (without the quotes) into the body of Section0001.xhtml.
3. Add a new text item.
4. Open Section0002.xhtml and select code view, enter "<p>mongoose</p>" (without the quotes) into the body of the file.
5. Switch back to Section0001.xhtml code view, open the find dialog and type "mongoose" (without the quotes) into the Find what box. Choose to Look in all HTML files. Options are: Normal search mode, Direction all, no other boxes ticked.
6. Click find next.
What should happen:
Sigil should find the word in the second xhtml file, switch focus to that file and highlight the text.
What actually happens:
Sigil reports that the search term cannot be found even though the text is definitely in the epub.
Workaround:
7. Add a new text item to the end of the list (there are now 3 xhtml files in the epub, the last one has not been modified).
8. Switch back to Section0001.xhtml code view, open the find dialog and type "mongoose" (without the quotes) into the Find what box. Select to Look in all HTML files. Options are: Normal search mode, Direction all, no other boxes ticked.
6. Click find next. Sigil locates the relevant text in Section0002.xhtml.