Software Deployment

I am trying to set permissions on some registry keys in an MSI project using Dev studio 9.
On the reg key, and under the file permissions tab, I am setting the permissions like so:
Domain = fareham.gov.uk
Users = AllUsers

When looking at the sub keys permissions within Dev Studio these appear to be cascaded down, which is what I want.
However, when the MSI is installed it sets the above permissions onto the main key but the sub keys don't install at all?? [:@]
Has anyone else experienced this problem? Should I be setting permissions, file, reg key or otherwise in a different way?
We deploy our MSI's via GPO could it be done there instead?

Any help appreciated.