Since the next version is still weeks away, here is a patched one which solves this specific problem:
http://vaemendis.net/ubooquity/downloads/beta/Ubooquity-1.7.7.zip

Interesting, although I still don't understand why the working directory is "/root/".
Do you have other files created by Ubooquity in the "/root/" folder (like "cache", "logs", "preferences.xml"...)?

In any case this problem will be solved by this feature: http://ubooquity.userecho.com/topic/794934-when-using-duserdir-switch-a-few-oddities/.

If it appears in theme selectors, it means the new folder exists somewhere on your system.
The somewhere is supposed to be the directory from which you launched Ubooquity, but I assume you have already checked there.

Perhaps you could try to do a "find" on your whole system to locate the newly created directory ? (it has the name you gave to the new theme).

I still have no clue as to why this happens (perhaps some symlink or Linux user right combination I have not anticipated), but knowing where the new dir is created would help.

Fair enough, I'll try to implement a proper user dir switch. :)

Disclaimer: I don't know anything about Unraid, so my question might be stupid.

Assuming Ubooquity is launched through a script by the plugin, wouldn't it be possible to use a variable for the working directory that would allow the user the same flexibility as an explicit command line argument ?

Something like:

cd $MY_UBOOQUITY_WORK_DIR
...

I'am asking because using the "user.dir" setting is not a completely reliable solution (hence the bugs you encountered). So if there is a real need for a working directory setting, I'll implement it in the code itself. But I really want to be sure that this work is required as for all use cases I have been told about (except perhaps yours, hence my questions), the "cd into another dir" method was enough to solve the problem.

You're right, there is a problem with the webadmin.cred file.
I will probably fix it. However you can easily (and in a more reliable way) ensure that all files will be created in a specific directory by going into this directory before launching Ubooquity.

For instance if Ubooquity.jar is in /home/pi/apps and you want it to create its files in /home/pi/data, just "cd" into "data" before calling java:

cd /home/pi/data
java -jar /home/pi/apps/Ubooquity.jar

Much easier and safe.
Let me know if you have a use case that can not be solved this way (really curious).

Yes it's on my todo list, not at the top yet, though.

That's the bug I was talking about (the log directory problem).