Zen Cart can only detect based on what the server tells it when it asks about certain information. In this case it's getting the wrong information back from your server, which probably speaks to the idea that your server has some fancy nonstandard configuration going on, perhaps specialized mapping happening in the vhost configuration or whatever. That's all up to your hosting company's server admin, and untouchable by you or by the Zen Cart software.

However, it's really no problem at all, since when you're in the install screen where it presents you with the detected path, you can easily type in the correct path and carry on with installation. There's no "program" or "module" required to modify the paths. You simply use your own keyboard.