The advanced system tweaking doesn't touch that, do you mean the Windows Repair All in one?
If so that is normal. The Repair WMI tool is what does that. The WMI is used to write to tell the action center. Since the WMI is rebuilt the section that the antivirus wrote to it is gone. But after a couple of reboots or a update is done in the Antivirus the antivirus program will write to the WMI again and put it back
I was trying to find a way to read and store that info in WMI so I could have the repair program put it back to avoid the confusion to users. But I couldnt find any docs on it yet.
Shane