In the Scheme Compare, the Select Objects window filters only the desired objects to be compared by clicking on the “Add” icon. However in the resulting Advance Search window, if the option “Assemblies” is checked, running the compare may cause the compare to hang at the progress bar and not finish.
WORKAROUND:
Uncheck the "Assemblies" box, and continue with the Compare Schema.
STATUS:
Waiting for fix in a future release of Toad for SQL Server.