Set the separator as a double new line (%NL;%NL. It appears that Daffodil treats the 2 new lines as one. I see the same issue in CLI and JAPI.

Part of the DFDL:

<xsd:element name="TopLevel">
<xsd:complexType>
<xsd:sequence dfdl:separator="%NL;%NL;">
<xsd:element name="MessageHeaders" dfdl:lengthKind="delimited"
type="xsd:string"/>
<xsd:element name="Body"
type="xsd:string"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>

Input:

Date: xsw, 15 Feb 2013 08:54:52 -0500
From: john@doe.com
To: jane@doe.com
Message-ID: <OFB0B2662B.92FC9941-ON80257B1F.0045CE19-80257B1F.004ADB2A@doe.com>
Subject: Hello World!
Return-Path: <bob@smith.com>
Thread-Index: Ac3NbaI+1oo+ltP4SSqsh0WAhpIVagAAZVmwAALaigABACxfkAAPsjwAAA8SeAAABZb0A==
User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:16.0) Gecko/20120828 Thunderbird/16.0 Lightning/1.8b1
Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p

This is the body