For colorscheme files in particular, turning on syntax highlighting with "syntax on" will automatically re-apply your colorscheme, if you've set a colorscheme already.
So probably you applied your colorscheme before turning on syntaxt in your .vimrc. To avoid this you may be able to put your colorscheme command after "syntax on". But I'm not 100% clear on the complexities involved.
There may be different reasons for others of the duplicated files.