I had another look at the XML files and noticed something. The VST2 Search Paths shows as first and last path
C:\Program Files\Steinberg\Vstplugins
C:\Program Files\Steinberg\VSTPlugins\Native Instruments
Is maybe a double scanning an issue? I’m just speculating. Already with the first search path every subfolder in Vstplugins shall get scanned. Then the last path points to one of the already scanned subfolders. Could be that the scanner gets confused by that. Could you try with taking out the last search path? (And also delete the blacklist again)