After saving to file, the resulting file often has a few leading non-printable characters that cause problems when using those files as db scripts. They can be seen with various unix-like commands.
In the Save As dialogue prompt there is an option to set the encoding.
Verify that the "Save As" encoding is set properly.
Suggestion is to set to ANSI. If the file exists and was previously saved as UTF-8, and it is saved again as that existing file, it will stay as UTF-8.