Okay, I am not losing my mind. If you go to Edit --> Preferences, click on SQL Editor tab of Workbench Preferences, you will see a section towards the bottom called Query Results. The first check box in this section is Limit Rows and it was checked by default on my installation with a row count of 1000 so you should see something similar.
Uncheck the limit rows box or arbitrarily increase the 1000 to some other value.