It was a problem with filetype detection, this is the Pathogen issue.
The work around in my case was simple, use this to enable Pathogen:
set nocompatible
"execute pathogen#infect() " breaks filetype detection
call pathogen#runtime_append_all_bundles()
filetype plugin indent on
syntax on
What I did to find out was to remove my ~/.vim directory and start with a clean one. Adding things one by one and checking the results. I realized it was not detecting the correct filetype (when I opened an empty file detection was ok, but it was not when opening an existing file).