Unlike traditional antivirus programs that use definition-based detection, Malwarebytes uses a heuristic approach (behavior-based) to detect newer and unknown malware. So, the registry keys found by Malwarebytes kind of fit that detection modality.
I have gone and PM'd a malware expert, so help should be on the way. Please be patient, as malware experts volunteer their time here, and live in a multitude of different time zones. So, at times, it may be a little bit of ping-pong going on, but in the end, it will all work out.