I'm having a similar issue, but not just with the Repository module.
Logged in to DNN as admin or host, I can view the repository and the files it contains, but I get the Object Reference not set message if I attempt to access the Module Settings page. I have not been able to isolate this to security settings, as I was getting the same error both before and after I created security groups.
When I am logged in as a user with the security roll I will have when the portal goes live, I cannot access anything in the repository (I've checked the visibility settings, but can't get to the actual Repository settings). I can see the Dashboard and my header, but nothing appears in the Categories list, and the actual Repository module is not visible.
When I am not logged in at all, I can see everything that is in the repository, but I can't download (which is what I want for that security level).
I know that the viewing problem is more than likely related to an error in the settings, but I can't change the settings because of the error in the object referencing. It's extremely frustrating.
I have also logged a bug report for the Core team because I too believe it is an error in the core framework, as it affects more than one module.