I ignore if this is the same with the PDS (professional version) of LV...
With the FDS, after upgrading from 6 to 6.02, you need to copy the installation files of the application builder to C:\...\LabVIEW6\AppLibs\Install.
I suggest you to check if the files in this directory are correct.
However, this should not be a problem during the installation of your application. But at least when running the application you may encounter problems if the installed version of the application is 6 instead of 6.02.