Your comments

Yes Google fonts will work as they are not provided by the Ubooquity server but directly by the Google servers.

I have included the modification to allow fonts in theme in the next version (which is a few days away). I even allowed "eot" fonts, although I stringly discourage their use as they are only supported by IE.
Can't say exactly when the next version will be release (I'll try to relase a minor one in a week or two), but it will include a new attribute on entries that contain the current folder content:

<entry>
<title>Files in current folder (34)</title>
<id>293-files</id>
<updated>2015-03-19T21:52:59+01:00</updated>
<content type="html"></content>
<link type="application/atom+xml; profile=opds-catalog; kind=acquisition" rel="subsection"
href="/opds-comics/293/?displayFiles=true" pse:current-folder-content="true"/>
</entry>

Let me know if you want something different.
Like I said in my email, I did not find anything in the logs. Sorry.
I quickly tried Challenger Viewer in folder mode but I was not able to reproduce the problem.
Anyway I would not have been able to do anything as I am not the author of this viewer. You should contact him directly.

Unless Chrome has some sort of auto-refresh mechanism, keeping a tab open on Ubooquity won't do anything as the communication only happens when you are downloading something (the page, a file, an image...).
Once the page is displayed, the server (Ubooquity) does not know anything about the state of your browser.

I'd be interested in seeing the log files of Ubooquity for the period containing the shutdown (as a lot af things are logged when Ubooquity starts and stops).
You can send them to: tom 'at' vaemendis 'dot' net