Sequence goes as follows: (all actions performed by a single user with Admin privileges.)

1. Install version 7 of product
2. Install version 8 of product (Major upgrade, version 7 is removed, version 8 is installed).
3. Check box to launch program when installation completes. Program launches okay.
4. Close program
5. Launch program from installed start menu shortcut. At this point, installation goes into maintenance mode ("Please wait while Windows configures [product]). Program loads okay

This "please wait while..." message only appears once, when the user launches the product from the shortcut on the Start Menu. After this configuration completes, the message does not appear when the program launches.

I have enough understanding of how shortcut advertisement to understand that the shortcut is triggering a repair/maintenance event. What I don't understand is why this is happening. The appearance of the thing is that something is not being properly configured during the major upgrade, which is surprising since its, well, a major upgrade.

I have installation logs for each phase of the process - The cause for this is not evident to me. Any insights as to what I should look for? Logs can be shared, if needed.