Just another question. Do you have multiple partition? (C:, D:. E:, etc)
If yes, then it most likely the viruses or malwares reside in any drives other than C: drive.
As we always aware, when windows done installing, it then initially search for any other drives, read it, and lettering it. But it also will read a folder named "System Volume Information" on each drive. The problem is most of recent viruses and malwares reside inside those system protected folders and manipulate windows to read and execute them.
My suggestion is before reinstalling windows try to delete any files or folder inside "System Volume Information" on each drive. It sometime can be reached using bootable linux system.
Hope that helps a little.
Edit: You have to know the folder also has some saved automatic or manual system restore data. When deleted, it will loss. But with newly installed windows, you might not need it anyway.