After working in Query Builder for a while, when I use the right click menu, I see multiple listings of the 'Remove Notes' item.
Waiting for fix to be released in a future version of Toad for SQL Server.
Here are steps to replicate:
1) Open the Query Builder.
2) Drag two tables into the QB that have a relationship. Make sure the relationships is shown with the line connecting them.
3) Right click on the diamond in the middle of the relationship line and select "Select all rows from <table>" for either table.
4) Right click on one of the tables and look at the menu and you will see only one "Remove Notes" listed. Do Step 3 a couple of time, for either table, and check the right click menu again. You will see "Remove Notes" listed several times.