I have a similar problem. I'm using RedHat Satellite server to deploy RHEL6 servers, and have configured a post-install script to fetch and install the correct agent installation script (install.sh). The agent version is 4.6.0, and I'm not installing the VSEL product at the same time (that is configured in ePO as a client Product Deployment task)
I see the exact same behaviour as you, Günther - missing files and default SiteList.xml
When I perform the exact same steps manually as are in my post-install script, everything works perfectly.
Any ideas, anyone?