Do you use MBS Plugin?
Because we recently got our own email sending functions which allow you to take attachments from either container or file.
Maybe that would help as a replacement of built in FileMaker functions.
The "Send Mail" help for FileMaker 13 says the following regarding sending attachments on FMS:
FileMaker Server scheduled scripts support sending mail via SMTP. However, if you attach a file, that file needs to be in a folder that FileMaker Server is allowed to export to. For more information, see Get(DocumentsPath) function.
Make sure your path and permissions are set accordingly.
We skip this issue entirely and use 360Works Email 2 as a server-side plugin for all our clients.