It is strange that you are suddenly suffering issues. It looks like the box hasn’t been updated for some time (since April). You could try running an update to see if anything improves and also there is a new stable release out that you might want to try. (I suggest installing on a separate SD card.)
I also have the problem sometimes. If I want to turn off the synth, after a certain time it then splits back into the main screen. If I try to turn it off again, it will work. I installed the latest (fresh sd) version 3 days ago and am absolutely new to this system.
Zynthian has a supervisor wrapper that detects the exit code of the core python code and reacts accordingly. If there is a bug in the python code then it may exit with the wrong code and result in unexpected results including showing the error screen, failing to reboot, etc.
I am working on some core refactoring which currently suffers from an issue with rebooting and shutdown. That has bubbled towards the top of my TODO list but it is likely that the changes / fixes I need to do may not filter back to the current stable release (due to the substantial changes in software architecture) so the issue may persist for a little longer. It will all get better soon though…