Your comments

Your ideas are interesting as they would not require that much work on my side. ;)
(as long as you write the text file or provide the images)

I'll think about it.
You're right, connecting to online services is something I will not do as it would add a lot of complexity for a probably disappointing result. One of the reasons is that as far as I know, there is no "universal" comics data service like the ones that exist for music, movies or TV shows. Comcis data services that I know (e.g. ComicVine) are only focused on specific countries/regions.
"Report/Request" feature
Communication between users is really far from the intended scope of Ubooquity. I prefer to focus on core functionnalities.

Ability to have all comics in 1 base folder without having select comics twice.
Done in 1.7.5 (check the advanced options).

When you are on a subsequent page and click on a comic then press the "Up" button, it takes you back to page 1.
That's the intended behaviour. Partly because the "back" button of your browser allows you to go back to the page you were coming from (although I understand that in some cases it would require several clicks), mostly because remembering your position when navigating several hierarchical levels requires extra work on my side.

Is there a way to re-generate files?
Not through the interface, but you can rename a file, rescan it and re-rename it with the original name. THe scanning process is quick when only a few files are modified.

Would there be a way to display "Series" information? such as; Plot, Release year, Issues, etc

Series informations is displayed for each comic book when the comic book files contains metadata (you can write metadata using ComicRack or ComicTagger). If you mean series information not linked to a specific file (like a folder containing the series), I suppose I could implement a few things like the ones proposed by Paul and Matthieu below. We'll see...
Ubooquity needs to have writing permissions on the working directory (the one from which the Ubooquity process is launched) so that it can write (among other files) the "webadmin.cred" file which contains the hash of the admin password.

Apart from that (and reading rights on the comics/books folders of course), I can't find any link between permissions and the problem you have.

Already on the todo list.
As usual, no promise on the delivery date though. ;)
Sorry for getting back so late. Unfortunately I still haven't a clue of what might be going on. :(