Quoting from FileMaker Help:
In the "Creating and editing scripts" entry:
The Run script with full access privileges feature only functions in the file in which the script is defined. This command will not override access restrictions on external files. For example, a script to delete records in File A that has the Run script with full access privileges option enabled will not delete records in an access-restricted external file File B.
One work around is to use Perform Script to perform a "run with full access.." script placed in the external file.
Another work around is to modify your privilege setttings so that "run with full access..." is not needed.