I if you have already tried solutions like this one Vim + Pathogen not loading help docs where you only add filetype off before calling pathogen infect and you still CANNOT generate the help tags, this hint might help you.
Pathogen is searching for the bundle folder under ~/.vim/bundle, and generates the helptags for every doc folder, where ~ is your runtime path. On Windows the default runtime path for vim is ~/Vim/vim73 which somehow confuses Pathogen, if you change the runtime path to the previous folder ~/Vim everything is fixed!
The runtime path variable in Vim is changed using the command:
:let $VIMRUNTIME = "puth_path_here/Vim"
Type :h $VIMRUNTIME in Vim for a more detailed explanation.