lost in limbo

My 16 year old son who was born in Mozambique app**** for his permanent resident visa as his mother lives in and is a resident of South Africa in October 2014. As of July 2 2015 we have had no communication or information despite contacting Home Affairs on a weekly basis. He has studied in SA since 2002 on a study permit. We decided this year to apply for his permanent residency instead of renewing his study visa not expecting that it would take 9 months. We have kept his temporary visa active by travelling every month out of SA but this time Home affairs at the border say he should ,leave SA and not return 'till he is granted his Visa. So now a 16 year old child is supposed to live in a foreign country with out his parents and drop out of school.. This situation is now intolerable and we are at out wits end. I understand VFS are just a processing centre but who else should I contact? Is it possible to actually visit Home Affairs and if so where?