Sometimes you may encounter the problem of unnecessary repairs of MSI while launching the shortcut in the same logged in user. Here is the way to troubleshoot this problem.
You can go to eventviewr (by typing eventvwr in Run command) then to applications and check the latest error message after repair. It will tell you which component is missing and because of which MSI went for self heal.
You can now check out this component in your package and see what the problem is. Maybe your keypath is a moving target for that component.