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 Visual Studio 2013 setup window appears with the message:
>"Please wait while Windows configures Microsoft Visual Studio Professional 2013"
This screen stays up for about 1 minute then disappears, and the project then shows as rebuilding successfully.
I have set the output window to detailed and don't see anything obvious listed there. The last line before the setup window appears is
Building file 'c:\ProjectPath\Debug\ProjectName.msi'...
After that the next lines talk about packing the necessary dll and files for the setup program.
I think that VS 2013 is missing a component that is required for setup projects but I don't know what it is.
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.
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
exists and the problem disappeared.