The <a> must be in a paragraph if I recall correctly. The correct usage would be according to XHTML rules:
Code:
<blockquote class="calibre5">
<p>
<a class="calibre6" href="../Text/MSF1_split_002.html#filepos496759">chapter one</a>
</p>
</blockquote>
For the second one I think the culprit is <br class="calibre1" /> Replace it by <br />. That being said, I also am very suspicious about the class identifier of <em>. That does not make much sense to me...