Taking a look at this and a couple other converted books, it looks like the most obvious difference is that in a purchased KePub the space between sentences is included in the next kobo span:
Code:
<p class="para"><span id="kobo.5.1">The Guild gardens stretched out before her.</span><span id="kobo.5.2"> The University building loomed to the right.</span></p>
While in a converted KePub it's between spans:
Code:
<p class="calibre8"><span class="koboSpan" id="kobo.14.1">Lorkin met the man’s eyes and shrugged.</span> <span class="koboSpan" id="kobo.14.2">“Hardly.”</span></p>
I'll take a look at fixing that as soon as I can, but I can't say how soon that'll be.