Well, the only way that can be explained is malware or virus. The System Restore probably turned the system back to a clean state but later the bug came out from it's hiding place to reinfect the system, and that place must be the System Restore points folder. You will have to disable System Restore at some point to delete the bug along with the folder contents, but that will have to be calculated for efectiveness. The first thing to do is modify the user permissions in the System Restore points folders so the security scanners have full access and are able to delete the bug/s.
First enable hidden files view in Explorer / Tools / View... mark Show hidden files and folders, next remove the check mark from "Hide protected operative system files (recommended)".. Next in the View tab, disable "Simple file sharing (recommended)" removing the check mark. Apply and OK.
Next. Go to Explorer C: Right click on the System Volume Information folder and select Properties / Security.. (repeat in every hard drive partition if any)... and grant yourself full control of the SVL folders according to the information in the link... that will make the SVL (SR) folder fully accessible for best scanning results..
Follow with a virus and a malware scans. If that doesn't solve the issue, you will have to Restore the System, allow the computer to boot for SR to complete, immediately reboot and logon in Safe Mode and disable System Restore, reboot the computer.
Set, View, Change, or Remove Permissions on Files and Folders
http://technet.microsoft.com/en-us/library/cc754344.aspx
Change file and folder permissions in Windows 7
http://answers.microsoft.com/en-us/windows/forum/windows_vista-files/how-do-i-change-folder-and-file-permissions/465f2b42-63dd-4486-8dd1-c870290efeed