Software Deployment

I have an MSI that needs to create HKCU keys and copy a file into the <user profile>\appdata folder for each user with a vbscript in a custom action. Right now my MSI kicks off a repair the first time a new user logs in to copy the keys and file. It works fine with normal users but when a non admin logs in via terminal services the repair fails with an error message stating that only administrators can add/remove or modify installations in a terminal services session. I get the same error using

msiexec /fu <GUID>

How do you handle repairs on terminal servers?