After some private messages back and forth Johnson sent me this which I accept as the solution:
Hi Bob,
Many thanks for sharing the App Options! It looks like when Inventor detect the files need to be migrated and also there are pending change due to out-of-context edit (change in reference files), Inventor will prompt to save. The settings are correct for PDM workflows. It is because you do need to make sure everything is up-to-date, save, and check in.
The logical reason to explain the “random” behavior is that for performance purpose, Inventor may not fully load certain components (created in prior releases). So, they may not need to be migrated and they are not prompted to save. However, after certain operations (editing), the files are fully loaded and they need to be migrated. All of a sudden, the prompt comes up.
Actually, there is no need to fully migrate the files. The data saved in prior versions can perfectly work fine without having to save on the current version, if there is no change. So, I suggest you may want to turn off “Prompt to Save for Migration” option. This may reduce the “random” behavior. Please check with your CAD Admin first and see if this is Ok per your company process.
Thanks again!
Johnson