Your comments

Agreed. I'll extend the "Folder exclusion pattern" option so that it allows exclusion of files in addition to folders.
Didn't know this one. I'll try it out (although not for reading comics as I read them on iPad).
I have not tried but I doubt it. CSS height management is much trickier than it is for width.
The goos news is that the new comic reader is almost complete and will be part of the next version.
It features "fit to width" and "fit to height" options (as well as an automatic split of double pages).
When you run Ubooquity for the first time, it creates a few folder and files in the directory from which you launched it. Among these directories (cache, logs...) there is the themes directory. That's where you unzip the themes you want to install.

If you have already run Ubooquity but you still have only Ubooquity.jar, then your working directory must be somewhere else. It entirely depends on the way you launch Ubooquity (especially if you use a script to do it).
I never commit on deadline for Ubooquity, but I'd say end of august (september if things go wrong) is possible.
Oh, ok.
By limited success, you mean you managed to run Ubooquity ?

Ubooquity itself doesn't care if you run on a x86 or ARM processor. It just needs Java (which has indeed different versions for x86 and ARM).
ARM Java for QNAP seems a bit complex to install, but still doable:
http://wiki.qnap.com/wiki/Category:JavaRuntimeEnviroment

Once Java is installed, Ubooquity can be run, although I don't know if QNAP NAS have specificities that has to be taken into account.
Thanks for all this info, it'll help a lot.
I'll investigate further asap (can't work on it this week).
Interesting, I have not encountered this error yet.

If this happens only for a specific file, could you put it somewhere I could download it ? (you can email me a link at: tom 'at' vaemendis 'dot' net)
If not, the name of the file would help. Also, do your server run with a non-english locale ? And do you access it directly or through a proxy ?

(I do not support Internet Explorer anyway, would be a waste of time given the lack of respect it has for standards)