Well, it seems that the biggest problem many of us face is that we are so used to plug and play stuff without any type of edits of the code itself. I've been doing enough WP that I can't go around not editing stuff.
The reason I had a problem was because I was implementing this in the middle of the night and was very tired to notice things I usually would.
Basically, and as you state in the directions everyone should read, some themes do not use a loop.php so we need to add/replace the existing code.
Furthermore, when I was messing around with the settings I disabled the
Markup Display: check box, as well as the
WP-Paginate CSS File: check box.
I then placed CSS into the themes directory and everything changed but CSS wasn't happening. Now what I did was manually entered what both those check boxes do when checked and everything started working. Others should make their life easier by reading directions and leaving those boxes as is because manually entering them is the same as letting the plugin work this out.
So what I ended up doing was deleted the code I figured I needed....
<div class="navigation"> and
</div> closing tags and let the plugin do it where it needs to.
I just remembered that the stock pagination works by calling for the nav class so I figured it needs something similar.
Anyway, people just read the directions and all will be well. If something isn't working, then after implementation make sure to SHIFT-Refresh your pages to purge cache. If after that still does not work, you will likely find your answer here, if not post your questions and one of us can help you.
Thanks for the great plugin Eric.