With both iSiloXC 3.x and 4.0, certain character entities are misconverted. A sample ixl file follows with one such offending document. Look at the first paragraph. With iSilo 4.0, I see text that reads "had neuroscience?indeed, all the life sciences?in a chokehold". If you view it in a browser, you will see that those question marks are actually em dashes.
The convertor for iSilo 2.x converts the document just fine.
<?xml version="1.0"?>
<iSiloXDocumentList>
<iSiloXDocument>
<Source>
<Sources>
<Path>http://www.firstthings.com/ftissues/ft0305/reviews/dembski.html</Path>
</Sources>
</Source>
<Destination>
<Title>Book review</Title>
<Files>
<Path>/tmp/foo.pdb</Path>
</Files>
</Destination>
<LinkOptions>
<MaximumDepth value="0"/>
</LinkOptions>
<ImageOptions>
<AltText value="exclude"/>
<Images value="exclude"/>
</ImageOptions>
<TableOptions>
<IgnoreTables value="yes"/>
</TableOptions>
</iSiloXDocument>