Did you try trashing, not only the Vst2xBlacklist Cubase.xml, but also Vst2xPluginsCubase.xml and VstPlugInfo.xml?
Just the blacklist. I’ll try dumping Vst2xPluginsCubase.xml and VstPlugInfo.xml this evening and get back to you.
As to the “Double Cubase in the Menu” thing…of note: it doesn’t seem to do anything adverse to the performance of Cubase. The left-most does nothing while the right-most will open the proper menu.
It can’t be cleared by by deactivating the plug-in that set it off nor quitting the Project and opening a new one. Only a complete relaunch of Cubase clears it.