Add these lines to .vimrc file which located on your $HOME directory (or create one if you can't find one):
" Switch syntax highlighting on, when the terminal has colors
" Also switch on highlighting the last used search pattern.
if &t_Co > 2 || has("gui_running")
syntax on
set hlsearch
endif
And for your Cygwin CLI, so you can see clearly. Add this line to your .bashrc file on your $HOME directory:
alias ls="ls -CF --color"
That's it.. restart your Cygwin, and you'll find the differences :)