ftplugin/c.vim , java.vim, vb.vim and others change the indentation settings making it impossible to use filetype plugins without indentation (since filetype plugins are loaded last, after any user vimrc file). Those settings should only be changed in the appropriate filetype indent scripts.
Hrm. These're all vim-supplied. Could you discuss this with upstream please? I'd rather not tinker with core files like these ones locally.