Hi M_Whitby,
From your information, i suppose that you are in ALM 11 patch 2.
The issue you posted is treated as a defect and was resolved in ALM 11 patch 3.
You can also try this: After updating the SQL Query edit window, ensure that the refresh button(between "delete" and "Generate" button) is clicked before generating the report.
Hope that this information is helpful for you.
Thank you and regards