Just an update on my previous post, I reinstalled Build 3946 using the "Everything In One Folder (Old Style)" option.
This put the Thumbs9.config file into the C:\ProgramData\ThumbsPlus folder and the
On side note, the only reason I reluctantly installed the latest build was that from what I could gather, the issue of the thumbnails refreshing automatically when an image had been moved into the folder had been addressed. Unfortunately this is not the case, you still have to move off the folder and then back for the new thumbnail to show.