Ok here is an interesting one....
While creating passage lists linked to notes files with KEYWORDS in the content area of the notes I noticed that searches were not coming up with words that I knew were in my notes files. I noticed that in my keywords (in content area) contained a misspelled word and that SEARCH was not coming up with anything AFTER this misspelled word in the content area of the notes file.
Hmm its like indexing couldn't deal with the misspelled word...so don't misspell.