Created three table data comparisons that had differences in data. In the Comparison Result grid, the bottom compare was check and synchronize wizard was opened. In the wizard, checked the "Generate SQL Script Only For" check box and left "1" as "percent top from" and "Next" was hit. No script was shown due to the low percentage number, however, when the "Back" button was selected to change the percentage value, synchronization wizard automatically checked the first table compare in the background grid. The script generated by the synchronization now includes the first table compare, which was not originally checked.
Increase the number of "Percentage from top" prior to hitting Next on the wizard.
Waiting for fix in a future release of Toad for SQL Server.