Include it as a support file on the source files tab and it will work fine.
You can also use the .ini file VIs or just a simple file create and write to let the application create the .ini file upon startup, that way if the application is renamed it will still have a valid .ini file (the hideroot key won't be read until the next time it is launched though). The .ini file is also nice to use for other configurations, not just the LabVIEW keys. Personally I use Inno Setup to create installers (http://www.jrsoftware.org/), free and much more flexible.
