That will be pamac-manager. There is no such thing as pacman-manager, because pacman is a command-line-only tool. 
This should not have happened. If pamac told you to reboot, then it should have rebuilt the initcpio(s), which does not appear to have happened here. But that said, libpamac — the core of the pamac system — has had issues over these last couple of days, and there have been several updates to correct those.
I would suggest using pacman — command-line — to correct the discrepancies. 
sudo pacman-mirrors -f && sudo pacman -Fy && sudo pacman -Syyu
This should normally pull in the updated kernel again, as well as the corrected versions of libpamac and pamac-cli, and it will rebuild the initcpio(s) — it will show you the output in the terminal.