It was for sure an SSH issue, but the only remaining issue is all the settings being wiped whenever the VM reboots now. I've made 100 changes in the last 2 weeks and just had to do a restart to increase RAM from 4GB to 8GB as issues weren't loading I guess because I had too much in there.

Anyways after the reboot, yet again it reset everything to the day of first install, only shows 3 libraries, even though I should have 6 and now it's rescanning 1000+ comics as though they are all newly added since the reboot just 10 mins ago.

Is there a proper way to shut down to retain this information?

Not sure if relevant, but I did just notice the Ubooquity.jar is still stored in /tmp/ where I downloaded it from, could running it from there be an issue?

New update, so far server has been stable since not running it through SSH, but just noticed the server wipe happened again. Only this time instead of wiping it to factory default, it wiped it to an earlier version with only 1 library, very frustrating, is there some way to save state of everything so I don't keep loosing all the work I'm doing?

Update, happens every 10 mins it looks like, I noticed my SSH connection drops at the same time, so may be that the java file is running from that login instance and when that drops it closes the server, I am testing this now through VMWare console and running in from there to see if it's stable and for how long.

It just happened again, disconnected, have a constant ping running and the server is not going down, but when I SSH back in it isn't running anymore and I have to restart it.