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I take it that the problem is the backup like to correct 'mistakes' that the mod has introduced. Do i need to deletee the backup folder everytime? or just the once?

Im not entirely sure but I think just once should do. 

You need to extract the game fresh.  The problem was that the old version would backup already modified files, potentially broken files,  then use those files. Some versions also didn't replace the back'ed up files with the new files so it'd potentially intermix versions.

Extract a fresh copy of the game, the entire game to a fresh folder,  don't mess with the backup folder. Run it, then click apply for mods.