Pathogen does not work for me. I am following Adam Lowe\'s hints posted here (and few more) without any success...
My vimrc:
filetype off
call pathogen
I was having a similar problem. Pathogen was loading some of my plugins while not all of them.
After some fiddling and wondering I discovered (I don't know if it's mentioned in the documentation) that in each bundle/'plugin_name' folder, there should be another folder called plugin that contains the *.vim file.
Then, when vim starts will look, not in bundle, but in those folders within bundle that contain a folder called plugin... and will create other folders (in each plugin folder).
So, if the plugin is just a .vim file make a folder for it...
instead of:
~/.vim/bundle/vimexplorer/vimExplorer.vim
you need:
~/.vim/bundle/vimexplorer/plugin/vimExplorer.vim
And everything works like a charm.