My first thought is: if terms are not found by index searching, are the terms which were not found indexed?
You can see if a term is indexed left below on your screen (status line) when your mouse is on a term. If your colors are standard, the color of such a term is black (not red).
If index search does not find all indexed terms is that wrong. I have experienced this sometimes - then there is somthing wrong with your index or database.
Menu Tools - Rebuild - Database can fix this.
Then there is also "Data search'. Not so fast but this option finds as well as indexed as non-indexed terms (Search Data = Alt+D). See Cardbox Help - Tab search - "Data Search".
Btw: (only) if you want full text retrieval, it is smart to set each field to "index all" in your database design (native format -field properties - index all).