WORKAROUND:
Carry over settings manually from older install into the newer install.
Settings are stored in (Windows 7) C:\Users\<personal folder>\AppData\Roaming\Quest Software\Toad for SQL Server 6.0. Migrate the settings from Toad for SQL Server 6.0 into the new Toad for SQL Server 6.1.
STATUS:
Waiting for fix in a future version of Toad for SQL Server.