Log in as root, change permissions on shutdown, halt and ctrlaltdel files located in the /sbin directory. chmod 000 these files. This would prevent another program such as init,
from calling reboot or shutdown by itself.
If this solves the problem, possibly move these files if not statically linked to libs, which I dont think they are, move these three files to another safe directory till you can figure out why this is happenning.
of course chmod 750 them back when "if" you call shutdown from the shell or UI.
maybe don't move them just chmod 000.