I have put new javascript syntax and indent files in my 'bundle' directory (I use Pathogen). I noticed that VIM loads both my new files as well as the standard files, in particular it loads the standard files after and I fear it may be overwriting the custom ones.
The VIM docs says it should not load the standard files if it found custom one first so I am not sure why this is happening.
This is what I see with the :scriptnames command, you can see the standard files (line 32, 35) after the customer ones (line 31, 34)
31: /usr/share/vim/vimfiles/bundle/vim-javascript/syntax/javascript.vim
32: /usr/share/vim/vim73/syntax/javascript.vim
33: /usr/share/vim/vim73/ftplugin/javascript.vim
34: /usr/share/vim/vimfiles/bundle/vim-javascript/indent/javascript.vim
35: /usr/share/vim/vim73/indent/javascript.vim