Comment # 6 on bug 1174412 from Fabian Vogt

Ok, so either a tool is lying or it's silently changed. Let's ask a third tool:
efibootmgr -v
bash -x /usr/sbin/shim-install |& tee shim-install.log
efibootmgr -v
reboot # Probably fails again
efibootmgr -v

if it's already broken after shim-install, shim-install.log should show why.