There should be no compatibility problems with saved SQL from 10.6 to 10.6.1.
Make sure that you have copied the files correctly. Close Toad, copy
“\User Files\SavedSQL.dat” from your old 10.6 installation to
“\User Files\SavedSQL.dat” on your new installation. Do not copy the
file into your “C:\Program Files…\Toad for Oracle 10.6\ClientFiles\User