Formatting or reinstalling windows is the VERY VERY last thing you do IF you can't get the computer working properly.
I have delt with some very tough viruses but I have not had to reload windows because of them. After some deep thorough cleaning, windows runs great.
I would never suggest to anyone that "its always good to reformat after cleaning a virus". What is the point of "cleaning" a virus threat if your going to reformat it?
I would suggest browsing you System32 folder to make sure those files are not there. It doesn't seem like they are though.
When you open the folder, go to TOOLs and click on FOLDER OPTIONS, then click the VIEW tab and make sure SHOW HIDDEN FILES AND FOLDERS is checked and make sure HIDE PROTECTED OPERATING SYSTEM FILES is NOT checked.
If the files are there and you can't delete them, Download Unlocker 1.7 to help you remove them.