I suspect you're missing an optional dependency. $ pacman -Si virtualbox-guest-utils | grep non-stock Optional Deps : virtualbox-guest-dkms: Guest kernel source modules for non-stock kernels It's likely that it will work as it does work for the host, https://wiki.archlinux.org/index.php/VirtualBox#Hosts_running_a_custom_kernel , IOW I guess you need to install "virtualbox-guest-dkms", then run # dkms install vboxhost/$(pacman -Q virtualbox|awk {'print $2'}|sed 's/\-.\+//') -k $(uname -rm|sed 's/\ /\//') and after that to load the modules.
