The Domino server API getEmbeddedObjects();
returns the wrong result (zero) when a mail containing an attachment (as embedded object) is sent from the script.
Attachments do not necessarily have to be embedded inside a RichText field. To quote from the designer-help:
If you need access to OLE/2 embedded objects that exist in a document but are not part of a rich text item (for example, because the object was originally created on the document's form), use the EmbeddedObjects property in Document.
Another source of your problem could be, that there are several "Body" RichText items you would have to check.
HTH