hmmm I checked mine and they are all where they should be.
So I downloaded the latest version direct from the website and you are correct - there are what appears to be duplicate files in the root and in the scripts folder. The newer versions appear to be those in the root.
I wonder if ronski accidentally put them in the wrong place during an update.
If you are impatient you could use the ones in the scripts folder (which is where they should be), and then let the program do an auto- update.
Best wait for ronski to confirm, but I dont think it would work properly if you use the ones at the root because afaik they have to be in the scripts folder.