1. It was a vendor MSI. When you repair it as a user it gives error since ISelfReg table is populated. Remove its entry from ISelfreg table and add it into SelfReg table.
2. Repairing application as admin and user shows different functionality this is because application consist of some APPKeys and trans keys which consist of Hex Value which could not be repair in User. Hence it is necessary to give permission to HKLM\Extended System Hives.