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 had the same problem. I tried every possible combination.
Finally I found that if I use mksession to save my Vim workspace and have it load on Vim startup, it made pathogen not load new plugins I put into the bundle folder.
After installing a new plugin I now always delete my session file and start Vim fresh and every plugin loads fine.
filetype off
set nocompatible
set laststatus=2
execute pathogen#infect()
syntax on
filetype plugin indent on