The only thing I can think of is that the default theme is still in your cache. The bits that are loading are from the -extras, which would override any active theme.

The shouldn't matter in this case. The ubooqity themes pull from the themes subfolder whereever it's installed. It's not still zipped is it? It needs to be unzipped.

Is there maybe an extra layer of folder? Like are the files in Ubooquity\themes\comixology2 or Ubooquity\themes\comixology2\comixology2?

Both would make an entry in the drop-down, but only the first would work.

*Edited*

You had a screenshot of the admin page, so you obviously chose the theme. What I'm seeing is it's still loading your cached comics.css. Try clearing the cache by holding ctrl and hit refresh.

Here you go! http://ubooquity.userecho.com/topic/1061595-comixology-theme/

I use Mylar to download/sort my comics, and it has some built-in support for Comictagger. So things get tagged as they get added.

Comictagger is also a stand-alone app here https://code.google.com/p/comictagger/. It can bulk tag your stuff fairly quickly.

I'm ironing out the last of the bugs in a comixology theme. You can accomplish a lot with the right css. :)

I've replaced a lot of images with css to give it the look I wanted. Once this is complete, I'll be sure to share.

http://imgur.com/a/3gEcz