[Alan Anderson]

You didn't say what programming language you're using. My advice in this post applies only to LabVIEW. If that's not what you use, ignore it.

When you copy a project's folder, the build destination doesn't change. You have to open the FRC Robot Boot-up Deployment properties and change the Information category to have the correct Local destination directory.

You are building the code by right-clicking on the FRC Robot Boot-up Deployment line and choosing Build from the menu, and then installing it on the robot by choosing Run as startup, right?