Thanks for the kind words.
If you can describe the exact sequence you use to reproduce the issue, it will help greatly.
For instance from a fresh start of Bible Analyzer what are the minimum steps needed to cause the notes to not display after you type them in.
If you open Bible Analyzer, type some notes, how are you moving to another a reference? By clicking in the Bible window on a verse, clicking on a verse/chapter/book button, etc.
Developer, Bible Analyzer
But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)