If you add files to subversion they are associated with a mimetype. SvnQuery will only index text files, that means files without an svn:mime-type property or where the property is set to something like “text/*”. At work I wondered why I couldn’t find some words that I know must exist. It turned out that subversion marks files stored as UTF-8 files with BOM as binary, using svn:mime-type application/octet-stream. This forces the indexer to ignore the content of the file.
After this change indexing worked again. I now run a daily query that ensures that no sources files are marked as binary.