So far it is actually Obama's State Department Inspector General who says Hillary had no permission and was wrong to set up this system.  

The FBI (last report in excess of 125 Special Agents) under Obama's Attorney General Lynch  is the one conducting the other investigation and who have given 5th Amendment  immunity from prosecution to the Hillary staffer who set up the system while employed by both her  and the State Department at the same time.  
 
You have to remember that the civil suit under the FOIA by Judicial Watch where the Federal Judge (appointed by Bill Clinton in 1994) wants to delve into that 5th Amendment immunity and Hillary's e-mails is totally separate from what the FBI is doing.   

He is the same Federal Judge who is assigned to the  case where the IRS 'lost' all those e-mails regarding conservative organizations.

In case you are curious, he also happens to be African-American.