Closing an explorer window creates bad registry entries!

This is an odd problem...I think! First post here btw!

I had a virus a while ago that loaded bad copies of smss.exe and winlogon.exe. I was able to isolate the files in safe mode and delete all the replicator apps and damage that it did. It was just adware and wasn't a big deal.

Those files are long gone, but the registry entires in HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run keep re-appearing. I shut down every service/executable I could without having windows crash. So I know there for a fact there is no program still running. It creates the entries whenever I close an instance of explorer (search, folder, etc.) . How can I stop that from happening?

Mike