Huh. My installs are stock pi stuff. The the extras I install:
- samba (just so I can ping it from a Windows environment.)
- mc (Midnight Commander, my cli file manager weapon of choice)
- unclutter: (hides the otherwise annoying mouse pointer in kiosk-y type applications)
This was written for an earlier version of Raspian/NOOBS, so there might be minor differences. VNC is running by default, for example. But VNC, and SSH are more of a convenience for me, than necessary to run a client.
You might also try deleting the .ignition folder to get a fresh download of Jython and your project.
Feel free to modify the attached guide to your environment. I wrote it so that somebody could set one up in my plant in the unlikely event I would actually have a day off. Sarcasm intended. 
Raspberry Pi Andon Client Setup.txt (2.7 KB)