I won't say it is not malware,,, but it doesn't exactly sound like it, that I am aware of.
I would not say these accounts carried over from an old install unless you didn't format the drive before installing the OS.
I do not believe these accounts would populate the registry, just by showing in the security tab of a folder on an external drive. But unfortunately I also can not say, it is not possible.
I would, at this point, (mainly because of what you were doing to the registry) backup data,,, pull the external drive off,,, reformat again the main drive,, and start over....
During the install,, delete the partition, reboot, then begin the install. This will hopefully make it believe there is nothing on that drive before beginning the install again. Could be cross corruption or something?
I am only guessing though.