[USERPROFILE] would be the folder I would use. This is set by the built-in InstallShield custom actions that pull this folder from the environment variable I was talking about.
So, based on your current configuration, I would expect this to work with standard AutoRepair. Now, msiexec /fup, again, should work OK for this. But there's a few things I would try to see if they make any difference:
1. Change /fup to /fpocmus. This is the standard parameter that's used for Autorepair when it gets called by a COM Class or Advertised shortcut.
2. Try running the repair from Add/Remove Programs to see if the same behavior persists
3. Use the link I posted to generate logs of when the file isn't getting copied. Basically, with the REINSTALLMODE parameters being set with /f, it will not be copying the file if it is looking in the wrong location. If it IS looking in the wrong locate, it should be visible when it determines that the component needs to get reinstalled.
If nothing seems to help, posting the log for review probably would be helpful. Something might be evident in the log that I'm overlooking.