Intermittent or seeming random problems are usually the most difficult to troubleshoot.
Unfortunately, I cannot replicate this problem myself which makes it all the more difficult to investigate.
If there seems to be no pattern in what configuration options trigger the problem, then perhaps there is a pattern elsewhere (for example with the number of images in the gallery) that might give us a clue as to the nature of the problem.
Try creating a Juicebox gallery with just a single image (or a couple of images) to see if this helps.
The problem could be due to a timing issue with the way that Lightroom builds the XML file for use in the live preview (although this is just speculation). Maybe under certain conditions, it takes too long to build the file, resulting in the 'Config XML file not found.' message.
If this is the case, then it might be very difficult to solve (as the live preview is essentially handled by Lightroom itself rather than any specific code in the plugin).
However, if you try using only one or two images, then there will be fewer <image> entries for Lightroom to process in the temporary XML file and it might make a difference.
Also, check that your version of Lightroom is up to date. The latest version is CC 2015.4 or 6.4.
An update could potentially help (especially is there is a bug in an older version which is somehow contributing to your problem).
Although the live preview can be very helpful, you should still be able to successfully create a gallery even if the live preview does not work.
I realise that this does not solve your problem but please try creating a gallery (by clicking the 'Export...' button) after the live preview window fails to see if the resulting gallery is OK.
Lightroom serves the live preview from a temporary folder. There is no real gallery folder until after you have exported the gallery to your hard drive (via the 'Export...' button).
The following is more of a workaround than a solution (if it works at all) but it might be worth trying to prevent you from having to change the 'Web' module's 'Layout' and lose your settings.
Open the plugin's 'index.html' file ('juicebox_pro.lrwebengine/index.html') in a plain text editor and add the following code just before the closing <body> tag on line 89. The line number refers to the current version of the plugin (v1.4.4.2).
It should display a 'Refresh' button in the top-left of the live preview window only (not in the exported gallery) which you can click to try to reload the gallery.
<% if mode == "preview" then %>
<div id="refresh" style="background-color: rgba(0,0,0,0.5); color: rgba(255,255,255,1); cursor: pointer; font-size: 12px; left 0px; padding: 4px; position: absolute; top: 0px; z-index: 9999;">
<span>Refresh</span>
</div>
<script>
$('#refresh').click(function() {
window.location.reload();
});
</script>
<% end %>
I hope the notes above help.