Your comments

Not sure if you can check it but simple replace it in the Java8 app.


Doesn't let you save the stop script? With which error?


And the script being done in 1 sec is normal. Check if Ubooquity runs via opening its website(In my script the port is 2204!). If it doesn't check the log and see if it crashed for some reason.


If the log again is empty I think something is wrong with your DSM Installation.

After updating to DSM 6 on my DS412+ I found out that you now easily could do it with the Task Scheduler (Start it at boot, manually and stop it). Wasn't working on DSM 5.*

Also check if you installed Java 8 x64 (not x86!)


This is how I start it manually and at boot (This can be simply copied into the Script Textbox):

#!/bin/bash
/volume1/@appstore/Java8/j2sdk-image/jre/bin/java -jar /var/packages/Ubooquity/Ubooquity.jar -workdir /volume1/Comics/Ubooquity/ -port 2204 -headless -webadmin > nohup.out 2>&1&


Stopping:

#!/bin/bash
pkill -f 'java -jar'

Hope this helps

@Emmanuel:
If I'm not mistaken @eaDirs are mostly empty. In which case it should be enough to check the "hide empty folders" option. Then there's also the "Scan exclusion pattern" option.

Provided link to NSFW Image via PM.
Finally also got to test this. Works now like it's supposed to. Thanks you two : )
Interesting. I don't restart my Server often but now I had to... I now have the same Problem : D
It almost seems like Synology deactivated/broke this via some patch because it worked before, but now it doesn't anymore.
You are welcome : )

Well, that's not good. In this case I would try to consult the Synology Forum or/and Support.
Autostart: hmm, no idea what the issue could be then. Have you tried placing another script in there and seeing if it runs? Or/And logging the ubooquity script to see if it is even executes?
Maybe also create a thread in the synology forum. Possibly someone else had a similar or the same problem (like someone else here in another thread).

Network loss: That's definitely weird. Synology stores its logs in /var/logs/. Maybe you can find a log there which can help find what causes or how it happens.
Hmm, then maybe try to place another script there, which does something simple as only writing a file somewhere. See if that works. It that too doesn't work I would try the Synology Support (or their forums).

SSH Script Start Problem: Add the following after all the switches when you start ubooquity: " > nohup.out 2>&1&"

Example:
nohup java -jar /var/packages/Ubooquity/ubooquity.jar -port 2202 -headless -webadmin > nohup.out 2>&1&