If you've used relative path references, these all change when you've built an application. This is because the VI is now inside an .exe, .llb, or .dll. If that's the case, you'll have to do an extra strip path. You can check this by doing a development distribution to create a .llb that you can debug and check the paths. To make a program work in both development mode and as a built application, you can add some code to detect either condition. What I do is use an Open Application Reference and then an Application Kind property node. The property node will return Development System, Run Time System, etc.