I have recently upgraded to Visual Studio 2013 (with the installer extension installed) from 2010, and now when I rebuild my Visual Studio Installer project, a
Just adding as an answer here, as it might not be clear in comments above.
Based on @Glytzhkof's answer, checked the Event Log and found that a folder was missing.
Make sure the folder
C:\Windows\Microsoft.NET\Framework\URTInstallPath_GAC
exists and the problem disappeared.
This should at least make you certain what component in the MSI that is triggering the self-repair. Most MSI packages can be repaired, but the Visual Studio installer works in mysterious ways. Give it a shot.