I had this issue with the first test lab I built, and now I'm having the same issue again with the second lab.  Basically, I do not have access to the SMS_<site> folder and subfolders that are automatically created. I believe this affects application and OS deployment.  Also, I cannot view logs because of this. 
  
I followed several tutorials (including this one) to install SCCM 2012 and this happens. The account I'm using is a domain admin that is also in the local administrator group on the SCCM server.  The only account that can access this folder seems to be the built-in 'Administrator' account (local and domain).  This is unacceptable should we deploy SCCM on our production environment. 
  
I've only gotten as far as creating a boundary, a boundary group and discovery methods. I don't see how I can go any further until I have access to this folder.  Any help would be appreciated.  Thanks.