I added the line:
iPosition=88;//stop processing until restarted by finding a blank line <br/>
towards the end of the agent Process Incoming Alerts just after it saves the document so the end of it reads:
strEmailTextLine = new String(stEmailText.nextToken());<br/>
strEmailLinkLine2 = strEmailTextLine.substring(0, strEmailTextLine.length() - 2);<br/>
} else {<br/>
strEmailLink = strEmailTextLine.substring(1, strEmailTextLine.length() - 2);<br/>
}<br/>
RichTextItem rtiLink = docNews.createRichTextItem("niLink");<br/>
rtiLink.appendText(strEmailLink + strEmailLinkLine2);<br/>
<br/>
//Now that the HTML has been harvested, save the document<br/>
docNews.save(true, false);<br/>
iPosition=88;//stop processing until restarted by finding a blank line <br/>
} else {<br/>
<br/>
//This is one of the story group lines that has the story abstract in it.<br/>
sbAbstract.append(strEmailTextLine + " \n");<br/>
}<br/>
}<br/>
}<br/>
}