Description:

When a new kernel upgrade is avaliable and the linux-headers package are also installed the upgrade order that pacman ahve is to install first the kernel and then the headers.

This way when the hook are rebuild for a new kernel version the headers are still not avaliable and if this hook needs the headers for this kernel this hook will fail.
As a workaround if you reintall the kernel right after the update(just simple run pacman -S linux) the hooks works ok as now the headers are installd.

For example if you have the linux kernel 3.8.8-1 you will have both the kernel and the headers on this version.
If a new kernel rolls out pacman found the new kernel and the headers for this package(lets say 3.8.8-2)
Pacman installs the kernel 3.8.8-2 and all the hooks start to rebuild but if some hook needs the headers for this kernel the ones found in the system are still the 3.8.8-1 and the hook failed because can not found the headers for this kernel.
After the kernel package is updated the headers update to the 3.8.8-2 but at this point the hooks depending on this already failed and will not be rebuild untill the kernel image is reintalled.

Proposed solution:
If the kernel headers are always installed before the kernel image the hooks will not have any problem to rebuild.