[huttdes]

So I assume there is actually only one movie.nfo those folders?
If there is, then can you zip up one of those movie.nfo files, and your config.xml file from Media Companion, and upload somewhere. Then PM me a link to download.
Alternatively you can go to sourceforge ticket site for Media Companion, open a ticket there and attach the files directly to the ticket.

And after that you can try, re-download MC and extract to a different location, add a movie folder source and refresh. See if these movies double up again. 

 Good catch.  For whatever reason there were TWO .nfo files in all the duplicate entries.  One being labeled as movie.nfo and the other being listed as MovieName.nfo  

Deleted both NFO files in all the duplicates (also changed the setting to advance so it would save it as moviename.nfo)  Refreshed the DB, movies disappeared.  Scan for new movies, it picked up all the duplicates wrote new NFO files, refreshed again, duplicates are now gone.

I wish I could tell you HOW two NFO files got into those folders, but I can't. 

 Heh, sorry I saw your other posts but must have misread them. Could have helped you earlier as I had the same problem recently.
I'm assuming I got the issue from using different media managers in the past. I used MediaElch for some time and I believe it was set to scrap movie.nfo as opposed to <moviename>.nfo

So if you have used a different program in the past that may be why or if you changed settings before a rescrape like @"chrissix" said.