home config file in ~/.vimrc (this works everywhere except Geany) global config file in /etc/vimrc (this works everywhere except Geany)
It is almost certain that these are not hard coded paths, they will use environment variables. Thats why I suggested you `echo` them in the VTE to be sure those variables are set properly.
You didn't answer the question of how you were running Geany, menu or terminal?