First. If you want a good installation, make a copy of important docs, pictures etc, then perform a good reinstallation of the OS. Boot from CD, remove all partitions and make one (system) of desired size. Format it using NTFS ("normal" not "quick").
After reinstallation, do not plug in the internet cable and any other of your USB devices. Take a 100% clean USB drive & system and install all necessary drivers & Microsoft Security Essentials.
Make all patches & updates of the OS (approx. 300mb + 3 reboots), then create a system restore point. It would be perfect if you could make an image of the system disk (for example Acronis True Image, Symantec Ghost).
Download Panda USB Vaccine & heal all suspicious flash drives and then make a full scan of them using Microsoft Security Essentials.
Write me if there is be any problem in any of the suggested steps.
In safe mode you can also try Combofix.