Are all of your failure cases on XP/2003? I'm going to seek confirmation, but 
this appears to be due to a known bug that can't easily be fixed that doesn't 
affect Vista and newer platforms.
 
> From: alexey.lar...@jeppesen.com
> To: wix-users@lists.sourceforge.net
> Date: Fri, 22 Nov 2013 06:20:02 +0100
> Subject: Re: [WiX-users] Buindle Major Upgrade cause first msi uninstallation
> 
> I've uploaded full logs
> http://rghost.ru/50344410
> 
> -----Original Message-----
> From: Blair Murri [mailto:os...@live.com] 
> Sent: Thursday, November 21, 2013 10:52 AM
> To: General discussion about the WiX toolset.
> Subject: Re: [WiX-users] Buindle Major Upgrade cause first msi uninstallation
> 
> We would need to see all the logs.
>  
> Here's an overly simplified typical sequence for your scenario when 
> performing a bundle major upgrade:
>  
> Bundle v1 is installed, installing 1MSIv1 and 2MSIv1 ...
> Bundle v2 is installed. It adds a dependency on 1MSIv1 (since it contains the 
> very same MSI) and it installs 2MSIv2 (which itself removes 2MSIv1).  Bundle 
> v2 then tells Bundle v1 to remove itself.
> Bundle v1 then removes its dependency on 1MSIv1 (leaving it behind since it 
> still has a dependency [which happens to be Bundle v2]) and then removes its 
> dependency on 2MSIv1 (and if it had been left behind by 2MSIv2 it would also 
> remove it) then removes itself from the system.
>  
> What could go wrong? Based on the very small section of log you shared, 
> Bundle v2 didn't assert its dependence on 1MSIv1 (usually that happens 
> because of an install condition on that MSI in the chain, caused by people 
> attempting to avoid "reinstalling something already on the box"). Thus, when 
> Bv1 removes itself, it takes the MSI with it (because there were no 
> dependencies left).
>  
> So the interesting part of the log is during the Bundle v2 installation when 
> it plans 1MSIv1. You didn't share that part of the logging from the time that 
> 1MSIv1 was removed prematurely. If it happens again, look for that.
>  
> -Blair
>  
> > From: alexey.lar...@jeppesen.com
> > To: wix-users@lists.sourceforge.net
> > Date: Wed, 20 Nov 2013 12:38:58 +0100
> > Subject: Re: [WiX-users] Buindle Major Upgrade cause first msi 
> > uninstallation
> > 
> > I tried to make simple test, but was unlucky - it working good.
> > The bug is happens from time to time.
> > 
> > Below part of bootstrapper and interesting difference in the logs.
> > 
> > ======================================================================
> > ==========================================
> > 
> >   <Bundle Version       ="$(var.Version)"
> >           UpgradeCode   ="3776424C-BD59-47B9-8341-966E1AF70B63"
> >           Compressed    ="no"
> >           Condition     ="(VersionNT = v5.1 And ServicePackLevel >= 3) Or 
> > VersionNT > v5.1"
> >           DisableModify ="yes"
> >    >
> >     <bal:Condition Message="You must have administrator privilidges to 
> > install $(var.ProductName)">Privileged</bal:Condition>
> > 
> >     <BootstrapperApplicationRef 
> > Id="WixStandardBootstrapperApplication.HyperlinkLicense"/>
> > 
> >     <Chain>
> >       <PackageGroupRef Id="FirstMsi" />
> >       <PackageGroupRef Id="SecondMsi" />
> >     </Chain>
> > 
> >   </Bundle>
> > 
> >    <Fragment>
> >     <PackageGroup Id="FirstMsi">
> > 
> >       <ExePackage
> >         SourceFile ="uninstall_msi.exe"
> >         Cache      ="no"
> >         Compressed ="no"
> >         PerMachine ="yes"
> >         Permanent  ="yes"
> >         Vital      ="yes"
> >         InstallCommand='/uc {2B57EC44-E524-4292-AC5B-437C3F7EFAAF} /ver 
> > "5.2.0.0" /l /s'
> >         SuppressSignatureVerification='yes'
> >         />
> > 
> >       <MsiPackage
> >         SourceFile       ="First.msi"
> >         DisplayInternalUI="no"
> >         Cache            ="no"
> >         Compressed       ="no"
> >         ForcePerMachine  ="yes"
> >         Permanent        ="no"
> >         Vital            ="yes"
> >         Visible          ="yes"
> >         InstallCondition ="VersionNT >= v5.1"
> >         SuppressSignatureVerification ="yes"
> >         >
> >       </MsiPackage>
> > 
> >     </PackageGroup>
> >   </Fragment>
> >   
> >   <Fragment>
> >     <PackageGroup Id="SecondMsi">
> >       <MsiPackage
> >         SourceFile      ="Second.msi"
> >         Cache           ="no"
> >         Compressed      ="no"
> >         ForcePerMachine ="yes"
> >         Permanent       ="no"
> >         Vital           ="yes"
> >         Visible         ="no"
> >         InstallCondition="VersionNT >= v5.1"
> >         SuppressSignatureVerification ="yes"
> >       />
> >     </PackageGroup>
> >   </Fragment>
> > 
> >  
> > ======================================================================
> > ==========================================
> >  
> > Good log (FirstMsi wasn't removed):
> >     [0A04:0E30][2013-11-20T14:59:20]w327: Will not uninstall package: 
> > FirstMsi, found dependents: 1
> >     [0A04:0E30][2013-11-20T14:59:20]w328: Found dependent: 
> > {ae6f0e39-9e52-4fc1-b157-4f8ac333951a}, name: SecondMsi 1.0.1358
> >     ...
> >     [0A04:0E30][2013-11-20T14:59:20]i201: Planned package: FirstMsi, 
> > state: Present, default requested: Absent, ba requested: Absent, 
> > execute: None, rollback: None, cache: No, uncache: Yes, dependency: 
> > Unregister
> > 
> > ======================================================================
> > ==========================================
> > 
> > Bad log (FirstMsi was removed):
> >     [0840:08D4][2013-11-20T13:49:43]w208: Plan disabled rollback for 
> > package: FirstMsi, due to incomplete cache: Partial, original rollback 
> > action: Install
> >     [0840:08D4][2013-11-20T13:49:43]i000: Setting string variable 
> > 'WixBundleLog_FirstMsi' to value 
> > 'C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp\SecondMsi_1.0.1355_20131120134943_0_FirstMsi.log'
> >     ...
> >     [0840:08D4][2013-11-20T13:49:43]i201: Planned package: FirstMsi, 
> > state: Present, default requested: Absent, ba requested: Absent, 
> > execute: Uninstall, rollback: None, cache: No, uncache: Yes, 
> > dependency: Unregister
> > 
> > ======================================================================
> > ==========================================
> > 
> > -----Original Message-----
> > From: Blair Murri [mailto:os...@live.com]
> > Sent: Tuesday, November 19, 2013 7:15 PM
> > To: General discussion about the WiX toolset.
> > Subject: Re: [WiX-users] Buindle Major Upgrade cause first msi 
> > uninstallation
> > 
> > Need logs and your bundle's chain's sources to be sure, but the usual 
> > culprit is a condition on the MsiPackage.
> >  
> > In WiX, just because an attribute is there doesn't mean it needs to be 
> > used. Most of the time the default behavior is really what you want.
> >  
> > -Blair
> >  
> > > From: alexey.lar...@jeppesen.com
> > > To: wix-users@lists.sourceforge.net
> > > Date: Tue, 19 Nov 2013 13:48:23 +0100
> > > Subject: [WiX-users] Buindle Major Upgrade cause first msi 
> > > uninstallation
> > > 
> > > Hi,
> > > 
> > > I have bundle with two msi. Each of them is uninstalling during bundle 
> > > uninstallation.
> > > First msi isn't changing. Second msi - implement Major Upgrade.
> > > 
> > > OS: Windows XP SP3 x32
> > > WiX 3.7.1224
> > > 
> > > Bundle 1.0.0:
> > >   A.msi 2.0.0
> > >   B.msi 3.0.0
> > > 
> > > Bundle 1.1.0:
> > >   A.msi 2.0.0
> > >   B.msi 3.1.0
> > > 
> > > Problem: sometime after upgrade Bindle 1.0.0 -> Bindle 1.1.0 A.msi is 
> > > uninstalled.
> > > 
> > > The upgrade log has suspect line:
> > >   [0D60:0D54][2013-11-19T14:10:43]i103: Detected related package: 
> > > {DC06DB90-9092-46D7-9268-67D2A6244B60}, scope: PerMachine, version: 
> > > 1.0.1357.0, language: 0 operation: Downgrade
> > > 
> > > 
> > > Related links with same issue:
> > >   
> > > http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/Burn-u
> > > pgrades-td7582052.html
> > >   
> > > http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/Bootst
> > > ra
> > > pper-Upgrade-Issue-tt7579392.html
> > > 
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