Using a InstallScript Project results in directories [TargetDir] & []Windows

I have a InstallScript Project built using "InstallShield 2012 Spring". The project builds and installs as expected. The project does contain some scripts that change the [TargetDir] via a dialog box. When I upgrade this project to InstallShield 2013, the project builds without issue, but when I install, instead on the files being deployed to the Target Directory, directories get created in the same directory as the setup with directory names [TargetDir], []Windows and the files intended beneath.

I have view the build logs, and there is no evidence of a problem. Not sure where to go from here. I have revert back to 2012 Spring for now.

Brad