It looks like you may have a good possibility, Perderabo
The man page for shutdown has the following paragraph...
If shutdown is called with a delay, it creates the advi-
sory file /etc/nologin which causes programs such as
login(1) to not allow new user logins. Shutdown only
removes this file if it is stopped before it can signal
init (i.e. it is cancelled or something goes wrong). Oth-
erwise it is the responsibility of the system shutdown or
startup scripts to remove this file so that users can
login.
...as you say, the startup scripts should remove it but maybe
somthing was modified somewhere.
Way to keep those brain cells working!