Jeff,
I've included the dialogs for the application issues that came up when the installer runs. If I leave the Measurement Studio 6 Installer CD in the drive, it tries to run the installer from there.
On a hunch, based on the possibility that CVI needed to be 'repaired' I let the MS 6 Installer run. It did something (no dialog as to what), and then asked for me to register the install. Then quit with a request for a reboot. After that, repeated distribution builds completed without any popups. Restarting CVI caused the prompt for entering the Registration #. It appears that this has resolved the problem, As I no longer get the installer popup.