Spot-on! Having the Plug-ins folder in the main PMS folder must have been a one-time glitch. After uninstalling and reinstalling, everything is now back to normal. All the scripthost exes are running again.
Regarding this:
“Generally I would say not to remove them. Are sure there are newer duplicates. Can you provide an example of one or more of the DLLs that are duplicated.”
After uninstalling and reinstalling, all the old DLLs are now gone. So, it should be safe to delete them manually as well.