Why can't I find words that I ""know"" I indexed?
First, analyze your analyzer. AnalysisDemo code in this http://today.java.net/pub/a/today/2003/07/30/LuceneIntro.html article provides insight into the tokens generated from analyzers, and the subsequent terms in the index.
If QueryParser is in the equation, use the .toString method of the generated Query instance to see what it did to the entered expression.
Generally the combination of understanding the analyzer and the results of QueryParser tell the entire story.
Try using Luke to browse your index: http://www.getopt.org/luke/