Your comments

Hello Stephen,
to your issues:

1.: Have you followed the steps of the Tutorial from http://vaemendis.net/ubooquity/misc/synology-tutorial/? Especially "Connect with SSH" or "Troubleshooting"
2. Your NAS looses connection to your network (or just the internet) or "only" your apps (check the port forwarding on your router)? Is it connected via DHCP or a fixed IP. If DHCP, change it to a fixed one.
That was quick and alright. Again, thanks Tom.
huh, apparently Ubooquity crashed and after manually restarting it writes the log file again. Unfortunately not into the new user dir but the application dir...
So, after trying a few things I discovered the reason. I only accessed Ubooquity via https, obviously ; )
Problem is, after you specify a userdir java needs to know directly where the jks file is otherwise it won't know where to look if you only specified the file (thus java only looking in the main folder, which now changed. Copying over the jks to the new folder won't solve the problem).

However with this now solved I have a new one: Ubooquity doesn't writes a log anymore, which is quite important! Does Ubooquity also somehow need to know where to write the log to, and if so where do I specify this?

////Plus, killing the Ubooquity process and starting it again (not via the Ubooquity Webinterface) causes to loose its DB and writing a new one thus having to scan the whole Comic Collection again. What's up with that?////
On second thought: Scanner wasn't finished at that point...

Sanders:
I start/stop it via the sh script and yes those two flags are added, plus the headless one
Question: Do you know if I can somehow start/stop it via the Synology Webinterface? Used the Package before, but it hasn't gotten an Update so far.

Servantie:
Thanks, lost the settings (could have copied them over but decided to start fresh again), but I have very few setting so I simply reconfigured it.
Thanks for the Suggestions! Will try them out and report back.
Doesn't work for me (Also a Synology NAS). Ubooquity creates the files in my new directory, but I am unable to access the Server afterwards.