The page split is done using quite convoluted CSS properties combinations.
I am not satisfied with the way it is done, I'll very probably rewrite this part once I have found a more reliable way to split pages using Javascript and CSS (I'm thinking "canvas").

In the meantime you can try something with the column-count property.
Eg:

#group
{    
    -webkit-column-count: 3; /* Chrome, Safari, Opera */
    -moz-column-count: 3; /* Firefox */
    column-count: 3;
}

.rootlink {    
    font-family: "Oswald";
    font-size: 30px;  
    display : inline-block;
    padding: 5px;    
    background-color: #a6a6a6;
       border: #080808 solid 4px;
    color: #1a1a1a;
    width: 150px;    
    box-shadow: -5px 4px 11px 2px rgba(0, 0, 0, 0.75);
    font-weight: bold;
    -webkit-animation: fadein 1s; /* Safari, Chrome and Opera > 12.1 */
       -moz-animation: fadein 1s; /* Firefox < 16 */
        -ms-animation: fadein 1s; /* Internet Explorer */
         -o-animation: fadein 1s; /* Opera < 12.1 */
            animation: fadein 1s;
}

Yes, the URL you see are not directly related to the directory structure of your collection. Nothing's wrong here (the "185" is an internal ID Ubooquity assigned to this book during the scan).

This white an grey cover is the default one, displayed when Ubooquity was not able to find the cover in the book:


It should not happen on Epub files (if you have an example of non-working Epub, I'd be interested in seeing it).
Mobi files are another story: the format is not public (and not documented) so Ubooquity extracts all images it finds (using a very empirical process) and tries to guess which one is the cover. That's the best I can do for Mobi files.

As for the mixed covers (the problem solved by a refresh), I have it sometimes on my iPad, but I have never been able to understand why. Never had it on Windows (with Firefox or Chrome).
Do you have this problem only with Chrome or also with Safari ?
(I don't own a Mac, so investigating this one will be difficult)

Well, that's purely network setup (nothing specific to Ubooquity), so it really depends on your OS and network hardware.
Try taking a look at the following threads, they might give you ideas as to what settings need tweaking.

http://ubooquity.userecho.com/topic/626428-ubooquity-outside-locak-network-setup/
http://ubooquity.userecho.com/topic/701174-for-some-who-might-be-having-problems-serving-over-the-internet/
http://ubooquity.userecho.com/topic/526455-access-ubookquity-through-internet/

I'll need a bit more information to guess what's happening.
By "incorrect", you mean the cover of another book/comic ? Or a page of the right book but not the cover ? Or something else ?
Also, on what are you running Ubooquity ? A desktop (Windows, Linux, Mac OS ?), a NAS ? Are your file located on the same device or do you access them from a network drive ?

If you can, copy and paste here the your system infos (there is a link at the top of your admin page (if you use the web admin), and a button on the first screen of the GUI ("General"->"System info")).

That's the problem with big "Download" buttons. People tend to ignore the small lines above it. ;)
Glad it's working now.