Submodules which are not "plugin" but have scripts in "ftdetect" and "ftplugin", are not loaded with the pathogen script.
This is the list of scripts which are loaded in my vim: http://pastebin.com/zFVvi962
OS: Debian Squeeze
VIM Version: 7.2.445
Works with updated version of pathogen.vim and a call to pathogen#infect()
Pushed at my fork: https://github.com/crodjer/vimfiles