Thank you for the post.
Could you post a screenshot of the script? Perhaps, a few examples of subject lines that are failing? Is the script sending via a mail client or using SMTP server settings?
The "$" in FileMaker Pro 13 is used for script variables, so the symbol would need to be included between " " otherwise the program will be looking to populate a variable. The "%" is usually reserved by many programs to indicate a space such as in a URL.
After reviewing the script, I can provide more information or a possible workaround.