SQL*XL picks up the SQL in the following way:
 
When you start the SQL dialog and you have a cell selected with a comment that contains the SQL from a previous run, SQL*XL will take that SQL to use.
 
When you start the SQL dialog and you have selected a cell without a comment it will show the previous statement you have executed.
 
When you start the SQL*XL dialog and when you have selected more than one cell, the SQL will be taken from the contents in the cells.
 
In your case you had probably not selected the cell with the comment in which you edited the SQL. SQL*XL then opened the SQL dialog showing the previous SQL, the one that you had just modified in the note.
 
Hope this helps.