BleepingComputer.com: Hkey local machine run entries

I had a nasty trojan in my system (it ran it's own proxy server), and killed it with Malwarebytes. It seems to have also have disabled the ability to execute entries in "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run" As a temporary measure I have moved the entries to HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run to get them to execute again. I would like to restore the ablity of the system to boot these start up entries from the default location. Any ideas as to how this might have happened and how to reverse it? I already tried creating a new version of the key By exporting the entries and deleting the key and merging the .reg file after checking it for any surprises just in case it was in the key itself. I also replaced winlogon.exe to be safe. This is a good one and I am out of ideas.