I am having the EXACT same issue as described by Vikas, but I have reason
to believe that this breakage is caused by a recent Windows Update released
by Microsoft, because I tested packages that used to upgrade fine from one
version to the next (they are released in production and have been used by
customers without issues), and even those don't upgrade anymore.

The errors in the main bundle log file are:
[1760:2DC0][2014-08-22T12:12:19]e000: Error 0x80070642: Failed to perform
minor upgrade of MSI package.
[1760:2DC0][2014-08-22T12:12:19]e000: Error 0x80070642: Failed to configure
per-user MSI package.
[1760:2DC0][2014-08-22T12:12:19]e000: Error 0x80070642: Failed to execute
MSI package.

And in the specific MSI log file I see:
MSI (s) (A4:30) [12:12:19:495]: SECREPAIR: Hash Database:
C:\Windows\Installer\SourceHash{C5E60292-2E11-4FAE-883F-E548ECF032F7}
MSI (s) (A4:30) [12:12:19:496]: SECREPAIR: CryptAcquireContext succeeded
MSI (s) (A4:30) [12:12:19:676]: SECREPAIR: filename: Product.msi Stored
Hash Value:qifyrB1gltbWOyNTEPMp8gkQLOj80n1Vgs9hAkFUPeg= Current
Hash:ewxqrvKcJkUL0IxZgZeAoopceBPNACUkDakExnZTxbw=
MSI (s) (A4:30) [12:12:19:676]: Machine policy value
'AlwaysInstallElevated' is 0
MSI (s) (A4:30) [12:12:19:676]: User policy value 'AlwaysInstallElevated'
is 0
MSI (s) (A4:30) [12:12:19:676]: MSI_LUA: Elevation prompt disabled for
silent installs
MSI (s) (A4:30) [12:12:19:676]: Note: 1: 3
MSI (s) (A4:30) [12:12:19:676]: SECUREREPAIR: SecureRepair Failed. Error
code: 390FC9A18

After that it rolls back. It looks like it's trying to repair something
because the hash values don't match?

I have another test machine on which I will uninstall all Windows Updates
from the last week or so to see if it makes a difference or not. I'm
running on Windows 8.1 Pro Update 1 and all the latest updates including
the downgraded Upgrade 2. I also found this thread:
http://www.edugeek.net/forums/windows-7/140586-possible-issue-kb2918614-causing-overlapped-i-o-operation-progress-errors.html

Any suggestions/ideas on how to fix this?

// Sascha



On Wed, Aug 20, 2014 at 10:10 PM, vikasyv <vikas....@gmail.com> wrote:

> I am using a Bootstrapper Application to bundle the msi installer. Can this
> cause any problems? Here is the BA code:
>
>     <Bundle Name="Bundle-Name" Version="$(var.ProductVersion)"
> Manufacturer="CompanyName" IconSourceFile="$(var.IconSourceFile)"
>           UpgradeCode="UPGRADE-GUID" Copyright="Copyright String">
>     <BootstrapperApplicationRef
> Id="WixStandardBootstrapperApplication.RtfLicense">
>         <bal:WixStandardBootstrapperApplication ShowVersion="yes"
> ThemeFile="Installer-Theme.xml" LicenseUrl=""/>
>         <Payload SourceFile="$(var.PayloadSourceFile)"/>
>     </BootstrapperApplicationRef>
>     <util:RegistrySearch Root='HKCU' Key='SOFTWARE\AppName'
> Id="CheckInstalled" Variable="App_Installer" Result="exists" />
>     <Chain>
>
>         <MsiPackage Id=&quot;MainPackage&quot;
> SourceFile=&quot;&lt;MsiFileName.msi>" Vital="yes"
>             DisplayInternalUI="no" />
>     </Chain>
>     </Bundle>
>
> Thanks
> Vikas
>
>
>
> --
> View this message in context:
> http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/Issues-with-Wix-Installer-per-user-minor-upgrade-tp7596442p7596450.html
> Sent from the wix-users mailing list archive at Nabble.com.
>
>
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