Ok 
On my PC conky start only if I set
exec --no-startup-id conky
No magic conky autostart.
Your system work here until I reboot, then I have only the shortcuts but not my conky on the left. After using ‘conky’ in the terminal I got “my” conky back.
Did you install something else?
With a non-transparent background, everything is fine on the ISO, so I’ll leave it that way.
If the end user wants something different, he has to set it up himself.
Which is usually necessary anyway because of the different hardware conditions.