I had same issue on windows 2012 R2 server and SQL 2012 SP2 install base. I had to manually grant the nt service\SQLServerAgent rights as shown in this article: https://msdn.microsoft.com/en-us/library/ms143504(v=sql.110).aspx I didn't have to give special rights to Event log (I tested job failure writing to app log and it did without any custom changes). I wish the installer would just work. I did get an error on install and tried to have sql config manager update to same account again, but it didn't work.

HTH someone in future,

Chuck