note that this can cause more than one problems, since user is starting with different (less) privileges
reported: Autologin starts with missing privileges · Issue #45 · Obsidian-StudiosInc/entrance · GitHub
this sounds like an issue with the .service file or something similar, or just with your system, more specifically: with "staying processes". Make sure to close / kill all your apt tasks, background tools, etc... before to perform reboots. It worked fast the reboot for me in my tests on vbox with it
then, this sounds like the same privileges issue (and you mention autologin), since reboot is not allowed but e16 exits from itself, you are back to entrance
uh, that's confusing lol, I assume you can run it when you run it from a terminal. Does all the other startup applications are run?
logind? mmh... did you played with sysvinit or similar? im wondering if you have some extra packages installed that may conflict in your normal boot procedure